[[AC:Snakes (ophidiophobia), Reptiles (herpetophobia)]]
* The Spelunker from ''VideoGame/{{Spelunky}}'', being kind of an Indiana Jones {{expy}} hates snakes, too. Doesn't really seem to stop him, though.
* ''VideoGame/WorldOfWarcraft'' has a shout out in the form of an NPC with a strong fear of snakes who's named Harrison Jones, which takes Indy's last name and his actor's first name.
* The last line of a journal entry in ''Vesuvia'' that mentions the discovery of a charred snakeskin is "Snakes - anything but snakes..."
* Gemini Man from ''VideoGame/MegaMan3'' hates snakes. Not surprisingly, he takes massive damage from Snake Man's Search Snakes.
* Part of a certain side quest chain in ''VideoGame/TheLordOfTheRingsOnline'' involves retrieving some baby turtles from the work shed of a hobbit named Grobo Dogroot who happens to be deathly afraid of turtles. When you go to pick them up, each and every one is called "Grobo's Greatest Fear."
* In ''VideoGame/LEGOIndianaJones'', several puzzles revolve around Indy's fear of snakes. You have to get rid of the snakes with another character (and it's not as easy as attacking them, since they're often in [[GrimyWater deadly mud]]) so Indy will join you where his skills are needed.
* The Bishop of Southwark in ''VideoGame/FallenLondon'', who asks you to bring him deadly beasts to breed an {{Evil Detecting|Dog}} "Hound of Heaven", repeatedly reminds you "no serpents!" [[spoiler:Naturally, the Hound turns out to be just that -- a huge white snake with a devil-detecting gaze.]]
* In ''VideoGame/Diablo2'' when the Druid enters the Claw Viper Temple, he mentions he hates snakes.
* The Shieldbreaker from the Shieldbreaker DLC of ''VideoGame/DarkestDungeon'', though her fighting style is based on snakes, is absolutely terrified of them due to a traumatic encounter with one during her escape from a wagon bound for a horrible vizier that she was being sold to, which ended with her having to [[LifeOrLimbDecision cut off her hand to halt the spread of its venom and free herself from the wagon]]. On several occasions upon camping, she has the chance to have a nightmare about giant deadly snakes, which throws her immediately into Horror mode and draws any other heroes with her into it for the battle of their lives.
* ''VideoGame/AssassinsCreedOrigins:'' Bayek has a severe dislike of snakes, even quoting the Trope Namer in one quest. Understandable, since regardless of how strong Bayek is, those scaly bastards ''will'' take off an entire bar of his health in a single bite.

[[AC:Spiders (arachnophobia)]]
* Ryoh from ''VideoGame/{{Warbears}}'', to the point where he climbs out of a window and across a ledge, then through another window to avoid a spider.
* Ryu of ''Franchise/StreetFighter'', after waking up with a spider in his mouth once, has an intense dislike of spiders. He even lampshades it when fighting SpiderMan in ''VideoGame/MarvelVsCapcom3''
-->''Spiders... I hate spiders.''
* Ryo Sakazaki from ''VideoGame/ArtOfFighting'' and ''VideoGame/TheKingOfFighters''. It was a prank from his friend Robert (putting a spider in his mouth while he was sleeping) that caused it.
* From ''Franchise/ResidentEvil'', Claire Redfield has no problems gunning down zombies by the truckload. She dislikes spiders. Especially those seen in [[VideoGame/ResidentEvilTheDarksideChronicles Raccoon City and Rockford Island.]]
* Artur from ''VideoGame/FireEmblemTheSacredStones''. His best friend Lute once tried to help him... by placing spiders on his face when he was sleeping. Yep, Lute is special.
* Apparently Matt "Positron" Miller, current lead developer of ''VideoGame/CityOfHeroes'', is afraid of spiders in addition to clowns (see below). When [[VideoGame/CityOfVillains half of the game is jam-packed with them]], you gotta wonder...
* Various spirits from ''VideoGame/GhostMaster'' specialize in exploiting certain fears; one of them in a giant spider.
* One of the quests that you can do in Stormreach Harbor in ''VideoGame/DungeonsAndDragonsOnline'' involves a guy named Berne Jorn who's been afraid of spiders ever since he was a kid. The quest he sends you on, which is called "Arachnophobia," has you clearing the eight-legged bastards (including a huge boss-level one) out of his family crypt.
* ''VideoGame/PokemonBlackAndWhite'' have [[http://static.tvtropes.org/pmwiki/pub/images/595-596_9853.png Joltik and Galvantula]], who have Unnerve as one of their abilities. Said ability makes the opponent afraid and unable to use berries. How '''[[RidiculouslyCuteCritter Joltik]]''' has this is anyone's guess.
* ''VideoGame/{{Toonstruck}}'''s Drew Blank exclaims "Spiders! Why did it have to be spiders?" upon seeing a couple of them crawling on the wall.
* Bounder Boffin of ''VideoGame/TheLordOfTheRingsOnline'' is terrified of spiders, which you have to kill during the introductory instance for Hobbits in order to help him cut through Old Odo's Leaf-farm to escape a Black Rider.
* Farkas, an otherwise fearless warrior of Jorrvaskr in ''VideoGame/TheElderScrollsVSkyrim'', at one point refuses to go any further in the Tomb of Ysgramor after encountering giant spiders there due to his experience with them back in Dustman's Cairn.
* ''Franchise/MassEffect'':
** Tali is apparently afraid of spiders, judging by her reaction to the Gestation Pods hatching if you should take her along on Grunt's mission in ''VideoGame/MassEffect3''.
** Garrus also dislikes spiders, though to a lesser extent.
--> "If I ''never'' see another spider again, I'll die a contented turian. Unless they have spiders in the afterlife. ''[[Funny/MassEffect Damn]]''."
* Wilson from ''VideoGame/DontStarve'' hates spiders.
* Kormac from ''VideoGame/DiabloIII'' does not like spiders. At all.
* Petra from ''VideoGame/MinecraftStoryMode'' apparently has a thing against cave spiders, even referencing the TropeNamer. [[DownplayedTrope She takes on normal spiders earlier in the game with no hassle, though.]]
-->"Cave spiders. Why'd it have to be cave spiders?"

[[AC:Insects (entomophobia)]]
* Adelbert Steiner in ''VideoGame/FinalFantasyIX'', sort of. He's deathly afraid of oglops, an otherwise harmless insect. So is Blank, though not to the same degree (he says he "can't stand them", but is able to put up with them for the sake of the plan to kidnap the princess). Though when Blank's armour breaks and the oglops are released, both Steiner and Blank begin running around in a panic. Garnet/Dagger later fakes a fear of oglops in order to make her "ordinary girl" act more convincing.
** Steiner even punches [[spoiler:Regent Cid]] clear across the room and begins ranting ("Get that repulsive bug off the throne and call the Regent!") when he first reveals himself to the party, having been cursed with an Oglop body.
* Blathers the Owl from ''VideoGame/AnimalCrossing'' hates bugs of all sorts, as made obvious by how he reacts every time you turn in something for the museum's bug collection.
* Lyle Smithsonian of ''Videogame/MetroidOtherM'' really hates bugs. Guess what's invaded the Bottle Ship?
* [[ShrinkingViolet Florina]] from ''[[VideoGame/FireEmblemElibe Fire Emblem 7]]'' is terrified by bugs (a support conversation shows her panicking when a bee flies around her), among a few other things.
* Karol in ''Videogame/TalesOfVesperia'' is shown to be petrified of them when the party visits a forest teeming with insects. In a rare show of kindness, Rita gives him a can of bug spray, which becomes a skill called 'Bug Busters' for him.
* Noel Vermillion from ''VideoGame/BlazBlue'' is afraid of bugs, especially ones with lots of legs. [[FridgeBrilliance Keep in mind she's only five, even if she doesn't look like it.]] When one considers [[TheWormThatWalks Arakune]] uses them in his attacks, her battles with him are... an experience.
* The eponymous ''VideoGame/{{Pikmin}}'' flee in terror from otherwise harmless Mitites.
* Grendel in ''Labyrinths of the World 4: Stonehenge Legend'' is afraid of bees.

[[AC:Mice and Rats (musophobia)]]
* The Good Fairy in ''VideoGame/{{Ceville}}''. Obviously you have to exploit her weakness to solve a puzzle.
* Zelda from ''VideoGame/TheLegendOfZeldaSpiritTracks'' doesn't like mice. Used as a gameplay mechanic, as Link has to get rid of those rodents before she will move on. Understandably it comes up as the third part of the final boss fight where if she gets touched by one, she fall under Cole's control. This creates the amusing sight of an imposing suit of AnimatedArmor (which Zelda possesses) shivering in fear at the sight of a mouse.
* The title character in ''Nick Chase and the Deadly Diamonds'' announces at one point that rats are his one weakness, his Achilles' heel.
* Monokuma and Monomi in ''VisualNovel/SuperDanganRonpa2'' both reveal that they hate mice when the player approaches Nezumi Castle on the fourth island (which isn't supposed to resemble any castle from the ''Ride/DisneyThemeParks'', honest!). As such, they can't even go near it. [[spoiler: This turns out to be plot-relevant. Because Jabberwock Island is all a Virtual Reality simulation, the Future Foundation, the creators of it, decided to implement a failsafe if it all went pear-shaped. Anyone in the teacher role is made to be scared of mice so that they can't go anywhere near the castle, which contains the code to access the inside of the ruins, where the means of activating the Forced Shutdown lies]].

[[AC:Bats (chiroptophobia)]]
* ''Franchise/MetalGear'': Naked Snake has a fear of bats, and (by extension?) Dracula.
* ''VideoGame/MrDriller'': [[Characters/MrDriller Ataru]] is deadly afraid of bats, especially vampires.

[[AC:Cats (ailurophobia)]]
* Serge from ''VideoGame/ChronoCross'' was said to have this (though he's apparently grown out of it by the time the player controls him). Justified in that he was attacked and nearly killed by a panther demon as a small child. We learn later that [[spoiler: Serge's father, Wazuki, was turned into a cat-like form by FATE because that was the thing that Serge feared the most.]]
* Creepers in ''Videogame/{{Minecraft}}'' flee from cats and ocelots.
* [[http://www.uesp.net/wiki/Shivering:Ushnar_gro-Shadborgob Ushnar gro-Shadborgob]] in ''VideoGame/TheElderScrollsIVOblivion'': Shivering Isles. He provides a quest of getting rid of a ''Khajiit'' beggar ([[CaptainObvious which is obviously unavailable to Khajiit PCs]]). Even moreso on how he comments on the current events based on the stage(s) of the main quest, [[GeneralRipper thinking that cats and]] [[FantasticRacism Khajiit are the root of the problems]].
* Celine from ''VideoGame/AsdivineHearts'' absolutely adores domesticated animals but is also deathly afraid of them due to being attacked by a dog when she was a child. This is revealed in the game when the talking cat in the party gives Celine permission to pet him and approaches, only to be thrown into the wall by her reaction. She compensates for this fear by having a large collection of stuffed animals instead.

[[AC:Dogs (cynophobia)]]
* A short time into the events of ''VideoGame/{{Geist}}'', it is revealed that BigBad Volks's [[TheDragon Dragon]] Rourke is afraid of dogs. Close to the end of the game, Volks holds a meeting behind locked doors and gives specific orders to shoot anyone who comes close who isn't himself or Rourke. The solution is straightforward: [[BodySurf possess Rourke]]. To possess someone, you must first terrify him. Thus, you undergo a series of short missions for the sole purpose of getting a dog into the same room as him.
* Alessa Gilespe from ''Franchise/SilentHill'' was terrified of dogs, which due to [[spoiler: her and the town itself being a RealityWarper who brings fears and abstract concepts to "life"]] is responsible for several monsters you see throughout the series; [[VideoGame/SilentHillHomecoming Split Head]], [[VideoGame/SilentHill1 Groaner]], and possibly the [[VideoGame/SilentHillOrigins Caliban]].
* According to the Drama CD of ''VideoGame/GuiltyGear XX'', Zappa is terrified of dogs (then again, he seems to be scared of ''everything''). Guess what? One of the ghosts possessing him takes the form of a huge, hulking black dog.
* Frederick from ''VideoGame/FireEmblemAwakening'' is afraid of wolves due to nearly getting killed by one when he was younger. Even something that looks like a wolf, like a [[KillerRabbit taguel]], can trigger this.
* Tron Bonne, from ''VideoGame/MegaManLegends'', is afraid of dogs and was once chased up a street lamp by a dog.
* Marcus Fenix from ''VideoGame/GearsOfWar'' received his [[RuggedScar trademark facial scars]] from being mauled by guard dogs in prison, and has been nervous around them ever since.
* [[spoiler:[[TheBigGuy Daruk]]]] from ''VideoGame/TheLegendOfZeldaBreathOfTheWild'' has been afraid of dogs ever since they were a child. Zelda finds this very amusing.

[[AC:Frogs & Toads (batrachophobia)]]
* Lucca of ''VideoGame/ChronoTrigger''. Becomes awkward when it comes up immediately after they meet with one of the party members, a giant anthropomorphic frog.
* Refia of the 3D versions of ''VideoGame/FinalFantasyIII'' has a fear of frogs, which makes for a fairly amusing conversation the two times where you have to transform into one to enter a dungeon. It's even better if she is the character who has to cast the "Toad" magic.
* Volgin from ''VideoGame/{{Metal Gear Solid 3|SnakeEater}}''. The phobia is so strong that if you toss a live frog at him during your boss fight with him, he'll stop attacking you to kill the frog, allowing you to get a hit in.
* Cornet of ''VideoGame/RhapsodyAMusicalAdventure'' suffers from this. Unfortunately, frogs are hiding in every other container in the Marl Kingdom. Oh, and there's a kingdom of bipedal, sentient frogs.
* In ''VideoGame/TheLegendOfZeldaTwilightPrincess'', Midna is very grossed out by frogs and toads, to the point that she refuses to give you any hints when fighting the Deku Toad miniboss in Lakebed Temple.

[[AC:Slugs & Snails (molluscophobia)]]
* Ursula of ''VideoGame/BreathOfFireIV'' is utterly ''terrified'' of sea lice (a harmless bug). Especially hilarious as this ends up being revealed in a WhatDoTheyFearEpisode segment between her and [[EverythingsBetterWithPrincesses Nina]], and Ursula is normally a Type A Tsundere who tries to be tougher than most men...
* Carol Palecki in ''VideoGame/MitsumeteKnight''. It's one of the rare things that makes her lose her permanent GenkiGirl attitude [[spoiler:or rather, her permanent [[StepfordSmiler Genki Girl façade]]]]. Do ''not'' pull a prank of putting a slug on her, or [[PermanentlyMissableContent she'll immediately cut all ties with you]].

[[AC:Birds (ornithophobia)]]
* Shale loathes birds in ''VideoGame/DragonAgeOrigins'' due to its stint as a statue in Honnleath. [[spoiler: as a prank you can give her an unsquishable pigeon and [[WhatTheHellHero force her to wear it instead of armour, all the time]] with the Feast Day DLC.]]
* ''VideoGame/{{Portal 2}}'':
** [=GLaDOS=] comes to hate them. [[spoiler:During her stint as a potato, one picked her up against her will, escorted her to its nest and started pecking at her]], so she has good reason to be distrustful.
-->'''[=GLaDOS=]:''' [[AC: AAGH! BIRD! BIRD! KILL IT! It's evil!]]
** Wheatley also demonstrates a dislike for birds after he's attacked by one (perhaps even the same one [=GLaDOS=] had a run-in with). To be fair, he ''did'' break its eggs.
-->'''Wheatley:''' AAH! BIRD, BIRD, BIRD, BIRD!

[[AC:Flying (aviophobia) or Heights (acrophobia)]]
* All playable lawyers, save Mia Fey and Athena Cykes seem to suffer from this in the ''Franchise/AceAttorney'' series: Miles Edgeworth (who already has a Seismophobia to boot) needs Gumshoe to fetch him books from the higher up shelves, Phoenix Wright has to be led by his hand by his teenage sidekick when passing a bridge and breaks out into hysterical catchphrase-shouting upon boarding a Ferris Wheel and Apollo Justice can't ascend as much as 10 meters without starting to shiver like a dry pile of leaves.
* Alister, Lara Croft's NonActionGuy partner from the ''Franchise/TombRaider'' series, does not like heights. At all. They make him "positively nauseous," as he comments at one point in the Japan mission of ''Tomb Raider Legend'' where Lara is making a dangerous climb up a really tall office building.
* Blaze the Cat from the ''VideoGame/{{Sonic Rush|Series}}'' series is often implied to have a fear of heights, especially when they reach [[FloatingContinent Sky Babylon]].
* Emma, Hal's sister in ''VideoGame/{{Metal Gear Solid 2|SonsOfLiberty}}'' doesn't like heights when asked about it by Raiden, but stated it's preferable to Water.
* Bartz Klauser in ''VideoGame/FinalFantasyV'' has a fear of heights ever since he almost fell down from the roof of a two story house while playing hide and go seek. He reveals this the first time the party rides the wind drake, and Galuf physically hurls him onto its back. Later on, he hesitates before jumping off the relatively low height of Bal's drawbridge into the moat.
* As part of its many {{Call Back}}s to earlier ''Franchise/FinalFantasy'' games, Vivi Orunitia from ''VideoGame/FinalFantasyIX'', just like Bartz, has a fear of heights stemming from falling from a great height when he was young (specifically [[spoiler:falling out of the cargo ship]].)
* ''VideoGame/ChronoTrigger'' has the example of Golem Boss who, after Dalton summons on top of the wing of an airship, cowers in fear from the height, [[ZeroEffortBoss without attacking]]. If not killed quickly, he then runs away.
* In one mission in ''VideoGame/GrandTheftAutoIV'', Niko seems nervous about having to take a lift on the outside of a building to get to its roof. And in ''[[VideoGame/GrandTheftAutoSanAndreas San Andreas]]'', [[TheLancer Cesar]] refuses to get into a crane because he's afraid of heights.
* Leo in ''VideoGame/AWayOut'' fell out of a tree when he was eight and has had trouble with heights ever since. As a result, whenever there's a choice involving heights (going over or under a bridge, skydiving vs walking through a jungle, etc), he'll always prefer the option that requires him to be near ledges as little as possible. [[GameplayAndStoryIntegration It even affects his side of the screen, as his depth perception gets distorted the further off the ground he gets.]]

[[AC:Water (aquaphobia/hydrophobia)]]
* Franchise/SonicTheHedgehog displays a fear of water in some adaptations (such as ''Anime/SonicX'', for instance), though not actually in the Modern games.
** ''VideoGame/LegoDimensions'' shows Sonic having a borderline PTSDFlashback when he realizes he has to visit the [[VideoGame/SonicTheHedgehog1 Labyrinth]] [[UnderwaterRuins Zone]], complete with Sonic 1's infamous [[SongInTheKeyOfPanic drowning music]].
* [[VideoGame/EternalChampions Ramses III]] has good reason why he is afraid of [[KillItWithWater Water]]
* Raine Sage, ''VideoGame/TalesOfSymphonia''. An optional skit reveals that this is because when she was young and she and her family were being chased, she fell from a boat and nearly drowned.
* Raz from ''VideoGame/{{Psychonauts}}'', because of a family curse.
* ''VideoGame/MetalGearSolid'': Emma Emmerich is terrified of water thanks to a Childhood Trauma. Ironically, Hal stated she used to swim like a fish and it's hinted she could still do that.
* Ayako Katagiri in ''VisualNovel/TokimekiMemorial''. A fear very well known in the series' fandom, and milked for all its worth by the creators, [[BokeAndTsukkomiRoutine as antics-wise]], [[OddFriendship she's regularly paired with]] Nozomi Kiyokawa, the resident swimming-lover and champion (who, {{iron|y}}ically, suffers from a primal fear of her own, thunder).
* Lesley Lopicana in ''VideoGame/MitsumeteKnight'', a SpiritualSuccessor of ''Tokimeki Memorial''. She's an {{Expy}} of Ayako, but unlike her where the origins of her fear were never explained, we get to know how Lesley got this fear of water (long short story - that you can read in the game's [[Characters/MitsumeteKnight Character Sheet]], - it's due to a Childhood Trauma).
* The Dahaka from ''VideoGame/PrinceOfPersiaWarriorWithin''. [[spoiler: There's even an alternate ending where you [[{{KillItWithWater}} kill it with the Water Sword.]]]] Also, any sand monster in this game loathes water. Strangely, the ones in the [[{{VideoGame/PrinceOfPersiaTheSandsOfTime}} prequel]] can be fought in ponds.
* Chloe Valens from ''VideoGame/TalesOfLegendia''.
* CJ from ''VideoGame/GrandTheftAutoSanAndreas'' claims to be afraid of water at one point, after getting a [[{{Squick}} discarded condom on his face]] while swimming as a child. Ironically, he's the first character in GTA not to suffer from SuperDrowningSkills.

[[AC:Fire (pyrophobia)]]
* Rydia's fear of fire can be chalked up to Cecil and Kain's delivery [[DoomedHometown burning the village of Mist to the ground]] in ''VideoGame/FinalFantasyIV''. Very soon after, she's forced to confront this fear and cast fire magic to melt a wall of ice blocking the party's path to Fabul, as she is the only one capable of doing so.
* The dragon in ''VideoGame/{{Loom}}'' is afraid of fire, a fact Bobbin uses against her with either the Terror or Sleep draft to set her hoard -- transformed by him from gold into straw -- ablaze.
* It's hinted that Milla Vodello of ''VideoGame/{{Psychonauts}}'' is a pyrophobe due to [[spoiler:the orphanage where she worked burning down ''with the children inside it.'']]
* Heather in ''VideoGame/SilentHill3'' is afraid of fire. She comments that "it's scary somehow..."

[[AC:Other nature phobias]]
* One of the player characters, Rikku from ''VideoGame/FinalFantasyX'' has a phobia of lightning (astraphobia), which she gets over in the [[VideoGame/FinalFantasyX2 sequel]] by camping in an area in Spira where lightning is striking down nonstop.
* Earthquakes (seismophobia) -- Miles Edgeworth from ''VisualNovel/PhoenixWrightAceAttorney''. The first major crack we see in Edgeworth's stoic facade is that he turns into an absolute mess at the slightest of tremors. It's no better in ''Trials and Tribulations'', when [[spoiler: ''he passes out'' after an earthquake hits Hazakurain.]] It also extends to airplane turbulence (which can resemble tremors) and elevators. {{Justified|Trope}} in it being the result of a traumatic and tragic incident he experienced as a kid.
* Jonathan Ingram in ''VisualNovel/{{Policenauts}}'' is a cosmophobe by his own admission, and also appears to show some level of claustrophobia. This clearly doesn't work in his favour when he has to leave the Moon via a material transport relay. Depending on the players' responses to Ed, and how long it takes the player to make the decision to leave, it will extend the action sequence. The first time you beg Jonathan to enter the pod, he will refuse.
* Timbersaw from ''VideoGame/{{Dota 2}}'' has a severe fear of trees, to the point that he built a mechanized suit for the purpose of cutting them down.

[[AC:Clowns (coulrophobia)]]
* Barry Dejay in ''VideoGame/BackyardSports''. He plays worse on the Bling-Bling Brothers Circus in ''Backyard Basketball'' just because he is afraid of clowns.
* The players of ''VideoGame/CityOfHeroes'' often ask for a Clowns powerset for the Mastermind (pet summing class based on minion-commanding villains), but are denied because Matt "Positron" Miller, the lead developer, is afraid of clowns.
* Nathan Drake from the ''VideoGame/{{Uncharted}}'' series. At the end of ''VideoGame/Uncharted2AmongThieves'', [[spoiler: Elena]] asks him on a scale of 1 to 10 how scared he was that [[spoiler: she would die]], he gives it a 3 or 4. Guess what was at 10?
* Trevor Philips from ''VideoGame/GrandTheftAutoV'' hates clowns, which unfortunately are what he sees after sampling someone's marijuana.

[[AC:Women (gynophobia)]]
* Sexy Women (venustaphobia) -- Laharl from ''Franchise/{{Disgaea}}'' [[FaceYourFears He becomes a]] [[{{Irony}} beautiful woman in [=D2=]]].
* Lon'qu from ''VideoGame/FireEmblemAwakening'', which stems from [[spoiler: his guilt of feeling responsible for the death of a childhood friend]]. He'll eventually make an exception for whichever female you decide to pair him with (and his daughter, should he have one).
* Guy from ''VideoGame/TalesOfTheAbyss'', due to a '''VERY''' traumatic event in his childhood.

[[AC:Ghosts (phasmophobia)]]
* ''Franchise/SuperMarioBros'':
** Luigi is afraid of a lot of things, but most of all, he's deathly afraid of ghosts, Boos especially. Despite this, he has to fight ''hordes'' of them in ''VideoGame/LuigisMansion'' to save his brother, Mario. He finally, if only mostly, overcomes this fear at the end of ''VideoGame/LuigisMansionDarkMoon'', even going so far as to [[spoiler:adopt the Polterpup as a pet]].
** Yoshi is afraid of ghost ''houses'', so he stays out of them while Mario and Luigi explore them. In spite of this, two bosses in ''VideoGame/YoshisIsland'' and one in the remake are ghosts. Also in both games, one Yoshi's relay leg consists [[BornUnlucky entirely of fortresses]] while another has [[BornUnlucky all castles]].
* Yukari Takeba from ''VideoGame/{{Persona 3}}'' is also afraid of ghosts.
* When [[TheStoic Roxis]] was still a freshman during the early parts of ''VideoGame/ManaKhemiaAlchemistsOfAlrevis'', he was, er, ''traumatized'' (he was ''foaming'' at the mouth!) by Pamela, the school's resident CuteGhostGirl. Since then, [[GameplayAndStoryIntegration he would have a hard time searching for items anywhere that could possibly be haunted (ranked as Super Hard for him), which, incidentally, are ranked Super Easy for Pamela]].
* Luso from ''VideoGame/FinalFantasyTacticsA2'' revealed his fear of ghosts when the clan must defeat a group of Undead. Adelle teased him afterwards.
* Youmu Konpaku from ''VideoGame/{{Touhou}}'' is scared of ghosts -- which is ironic, because she just happens to be [[HalfHumanHybrid half-ghost]] herself, and has a CuteGhostGirl as a mistress.
* Tear Grants from ''VideoGame/TalesOfTheAbyss'' is scared of ghosts despite being a {{Kuudere}}.
* ''VideoGame/TalesOfVesperia'': Rita Mordio ''really'' hates ghost-ships.
* ''VideoGame/MetalGearSolid3SnakeEater'': Naked Snake is terrified of anything involving the undead. Bats make him think of Dracula, and merely mentioning Dracula is enough to give him nightmares. Because Creator/HideoKojima loves to screw with his own character's minds, Naked Snake gets to face the ghosts of ''every person he's ever killed in the game.'' It's a little unsettling for us, the players, but it's horrific for him. In ''[[VideoGame/MetalGearSolidPeaceWalker Peace Walker]]'', there are more ghosts in some bonus levels. When Chico, a fan of cryptozoology, starts describing an optional boss as an "undead dinosaur" brought back to life by Haitian zombie-makers, Snake's phobias kick right back in and he starts trying to rationalize it as just an "ordinary" dinosaur that happens to be skeletal and immune to conventional weapons.
* Ragna the Bloodedge's Joke Ending in ''VideoGame/BlazBlueContinuumShift'' reveals that he is terrified of ghosts. So his joke ending turns him and most of the cast into ghosts. It's canon too; he is freaked out by Sena, one of the personalities that make up Platinum the Trinity, when Sena threatens to haunt him for the rest of his life in an attempt to mooch a meal off of Ragna. To top it all off, the true form of the BigBad Terumi is a creepy grinning green ghost.
* Princess Pitts in ''VideoGame/ChibiRobo'' possesses a lady-like terror of monsters and the like. As Chibi-Robo, you can use a Ghost suit to help train her to overcome her fear, though it takes a while and she faints a couple times initially.
* Knuckles the Echidna of ''Franchise/SonicTheHedgehog'', at least in ''VideoGame/SonicAdventure2''.
* Chip from ''VideoGame/SonicUnleashed'', as seen in the short ''Night of the Werehog''.
* Judging from what she says about the Old Chateau (a place where Ghost Pokemon and actual ghosts lurk), Gardenia, the Eterna City Gym Leader from ''VideoGame/PokemonDiamondAndPearl'' has this phobia. (Oddly enough, if you challenge her with actual Ghost Pokemon on your team, it doesn't make any difference.)
* ''VideoGame/HometownStory'' has its physically extremely strong female blacksmith be afraid of ghosts.
* Ringo Andou from ''VideoGame/PuyoPuyo'' is REALLY scared of ghosts. The mere sight of Yu and Rei (who are harmless and just like having fun with quizzes and puns) is enough to have her scream in terror. In an ironic twist, she discloses that she's into paranormal phenomenons.

[[AC: Darkness (nyctophobia)]]
* ''VideoGame/AlanWake'': Alice has a crippling fear of the dark. And don't tell me you didn't flip on a few lights yourself after/while playing through the game.
* Daniel from ''VideoGame/AmnesiaTheDarkDescent'' has a bad fear of the dark after an incident from his childhood. Staying in the dark too long makes his sanity lower and causes hallucinations, blurred vision, and teeth grinding. Too bad they didn't have very good lighting in 1839.
* Wolfgang from ''VideoGame/DontStarve'' is afraid of the dark, which causes his SanityMeter to drop faster during the night.
* ''Nobody'' in ''VideoGame/LEGOLordOfTheRings'' can go into dark places without some light source; they back out shaking their head. This gets downright ''silly'' when you consider that Dwarves typically live ''underground'', and that Gollum is very well-adjusted to darkness and light actually hurts him. They should be fine in the dark, but no. You have to send Frodo (who carries a light) into a dark cave first so that Gollum can go in and climb up the wall that starts there.
* Hayato in ''VideoGame/FireEmblemFates'' tries to act mature and WiseBeyondHisYears and ''hates'' being treated like a kid, but a fear of dark places is his weak point. The ''Boo Camp'' [=DLC=] (fighting Faceless monsters on a dark mountain) even has him ''in tears'' during his pre-battle quote.

[[AC:Various Phobias]]
* Porcelain (porcophobia?) -- [[VideoGame/MonkeyIsland Guybrush Threepwood]]. Speculated to have been caused by being hit over the head with a porcelain vase in the [[VideoGame/TheSecretOfMonkeyIsland first game]]. The developers have said they added this just as a gag - after all, who is scared of porcelain? Referenced in ''VideoGame/TalesOfMonkeyIsland Episode 1: Launch Of The Screaming Narwhal'', when you have to pick up a porcelain action figure. Guybrush grits his teeth and reassures himself "Calm down, Guybrush, it's only a little porcelain..."
* AGAIN [[VideoGame/MetalGearSolid Emma Emmerich]] shows up on this list: she doesn't like sea lice at all. We also have Big Boss himself, scared of [[TheUndead vampires and zombies]]. This is a subversion in terms of the 'recurring obstacle' trope - vampires ''are'' in the series ([[NotUsingTheZWord in a]] [[OurVampiresAreDifferent form, anyway]]), but Big Boss never encounters one.
* Bald people: [[CuteBruiser May]] of ''VideoGame/GuiltyGear'' has an extreme fear of bald men, and can even sense when someone is bald, as shown during the Story Mode in XX when she runs into Dr. Faust (who, under the paper bag, is bald).
* [[VisualNovel/UminekoWhenTheyCry Battler Ushiromiya]] is terrified of any vehicle that shakes when it moves, as was his late mother Asumu.
* Flora, Layton's ward in the ''Franchise/ProfessorLayton'' games, is afraid of being left alone (monophobia).
* Artix, normally fearless paladin extraordinaire in ''VideoGame/AdventureQuestWorlds'', is utterly terrified of the color pink (which Beleen mercilessly teases him about).
* [[ShrinkingViolet Florina]] from ''[[VideoGame/FireEmblemElibe Fire Emblem 7]]'' isn't only afraid of insects, but is terrified by bows ({{justified|Trope}}, because as a flying unit, she is vulnerable to them) and suffers from a mild case of [[DoesNotLikeMen androphobia]].
* All dwarves in ''Franchise/DragonAge'' (apart from those born on the surface, obviously) tend to have some fear of the sky (possibly Agoraphobia or Ouranophobia) due to the vast majority of them living in underground cities. They fear that going to the surface will not only make them lose their 'stone sense', but that they will fall ''up'' into the sky (this is called Casadastraphobia). Of the three dwarves you can recruit, one is a surfacer anyway, and the other two overcome their discomfort fairly quickly. Anders the mage appears to have claustrophobia, given his comments whenever you venture to the Deep Roads in ''VideoGame/DragonAgeOriginsAwakening'' and ''VideoGame/DragonAgeII''. There are also plenty of people who are terrified of mages/magic/demons, and of those, plenty are justified.
* In ''VideoGame/{{Ib}}'', Garry is utterly freaked out by all the blue dolls. Can't blame him considering one of them stalked him down a hallway and there was another time where [[spoiler: a whole bunch of them captured him and forced him to play a game with them]], but he found them disturbing even before any of them did anything.
* In addition to fearing sexy women (see above), [[VideoGame/DisgaeaHourOfDarkness Laharl]] is also horrified by declarations of love and positive thinking. He's mostly over it by the end of the game.
* Parodied in ''Deadfall Adventures'', where James Lee Quatermain's nonhuman archnemesis is... ''[[EverybodyHatesMathematics math]]''. Naturally, he comes across not one, but two puzzles involving math -- in the Mayan numeral system, no less.
* According to Mordin Solus in ''VideoGame/MassEffect3'', Urdnot Wrex, [[ProudWarriorRaceGuy krogan]] badass [[spoiler:and leader of his people]], is AfraidOfNeedles.
* The Rattled ability introduced in ''VideoGame/PokemonBlackAndWhite'' likely runs off of this trope, since the attack types that activate it--bug, dark, and ghost--are common phobias.
* After reaching the Empty Room in ''Maze: Subject 360'' the villain appears out of nowhere and asks which is the main character's greatest fear. You get to pick from a list which consists of nyctophobia, claustrophobia and fear of injury.
* In ''VideoGame/BaldursGateII'', the elf Aerie is claustrophobic. When the party finds that the BigBad has fled through a magical portal, one character speculates may very well lead into the Underdark, an underground world evil enough to compete with hell itself. If Aerie overhears this, she immediately freaks and makes it ''very'' clear that she doesn't want to go there. Guess where the whole of the next chapter takes place...?