In the Black Blade series, protagonist Lila Merriweather is the first cousin of Deah Draconi, the Big Bad's White Sheep daughter.
Jerin and Princess Ren in A Brother's Price find out that they are third cousins, sharing great-great-grandmothers. His grandfather was thought to be lost by family, but instead had been abducted and married to his grandmothers. This relation is distant enough that it does not hurt the romance, and in fact the Royal Blood that Jerin thus possesses means it's possible for them to marry.
Bud, Not Buddy has an orphan Gene Hunting for his Disappeared Dad, who he thinks is famous bandleader Herman E. Calloway. He is eventually united with Calloway, who turns out to be not his father, but his grandfather. His mother ran away from him in her late teens, and her father never learned what happened to her until Bud showed up.
Catwings: In Catwings Return, Harriet and James return to the city. They find a lost winged kitten who turns out to be their little half-sister.
The Chronicles of Dorsa: Joslyn finds out in book two that her older sister Tasmyn, whom she had been separated from as a girl, is still alive when they meet while she's dreamwalking.
Played to a ridiculous level in the WuxiaDemi-Gods and Semi-Devils with the protagonist's father, Duan Zhengchun, being a big case of The Casanova. Every singleLove Interest his son, Duan Yu, meets in his journey turns out to be his half-sisters. Though this is subverted later on as Duan Yu isn't Zhengchun's son, thus resulting in Duan Yu marrying all of them.
In Doctor Sleep, Danny and Lucy discover they're half-siblings, sharing their father, whom the younger sibling never met.
In Doctor Zhivago, Yuri Zhivago learns that his deadbeat father had an illegitimate son with Princess Stolbunova-Enritsi named Yevgraf. Later on, Yevgraf ends up being an important but enigmatic character, helping Yuri and his loved ones to escape most of the chaos brought on by the Russian Revolution.
Harry Dresden discovers fairly early in his adventures that he has a long lost half-brother, Thomas.
In Changes, he discovers that he has a long lost daughter and grandfather as well. Where it gets tricky is that it makes Ebenezar Thomas' long-lost grandfather, something neither of them are aware of (and might not be happy to find out). Harry's pretty careful about who he tells what: as of Skin Game, nearly everyone knows he has a daughter, but good luck keeping track of who knows about Ebenezar and/or Thomas.
In Empire of the East, the Lady Charmian's long-lost younger sister is unknowingly serving her as a handmaiden. Each of them lost their memories of the other as the result of encountering a demon as young girls. Well, "encountering" might be too mild; their father gave them to it as his pledge of loyalty- the demon allowed them to live for its own reasons...
In Ender's Shadow (the parallel novel to Ender's Game) we find out the backstory of Bean, a super-smart little genetic experiment who was kidnapped as an embryo, escaped captivity as a baby, and made it to the orbital battle school as a small child. He managed to forge a real friendship with exactly one other person in the school, who turns out to be the son of the people whose embryo was stolen, meaning Bean sought out and befriended his long-lost brother.
In Endo and Kobayashi Live! The Latest on Tsundere Villainess Lieselotte, Fiene is actually the illegitimate daughter of Lieselotte's father's older brother August and his fiance Elizabeth, making her and Lieselotte first cousins. The backstory is this: Elizabeth's parents vetoed her marriage with her fiance since he is dying, but the two decided to try to have their children anyway. After August's death and Elizabeth's pregnancy with August's child, she ran away to protect her daughter from her family, which is why neither girl ever learned about their family ties until Elizabeth arrives at the family manor. Lieselotte has her father adopt Fiene into the family to ensure her protection.
First Light: Peter and Thea are cousins. Peter's mother left Gracehope years earlier before coming back.
In Five Kingdoms: Crystal Keepers, The Hunter that is working for the High Shaper is actually Hunter Randolph, the older brother of the main protagonist, Cole. He actually got sucked into the Outskirts a couple of years before Cole, which is why Cole has no memory of him. (When somebody gets sucked to the Outskirts from Earth, those closest to them on Earth forget that they ever existed.) Of course, when Hunter tells him this, he believes it to be an elaborate ruse at first, especially since Hunter is working for the enemy. Hunter, however, provides enough evidence to make it very doubtful to both Cole and the readers that he could be anything but Cole's brother and then backs it up with deeds after he verifies that the shady stuff that Cole tells him about the High Shaper that the High Shaper had been hiding from him is true.
In The Five Little Peppers and How They Grew it turned out that the Pepper children's mother and their rich benefactor's son-in-law were cousins.
The plot of Fort Hope largely revolves around the protagonist, Greg, trying to get to know his long lost relatives. His love interest also ends up learning about relatives that she never knew she had.
Goblins in the Castle: Goblins on the Prowl has this as its big reveal — Fauna turns out to be Gertrude, the Baron's older sister who went missing when he was a baby, and rightful Lady of the Castle. It's as much a surprise to her as it is to the others, as she'd lost her memories when she was trapped in an unaging state. The Baron, for his part, is very happy to have her back.
In the eleventh Haruhi Suzumiya light novel, Fujiwara claims to be Mikuru's younger brother. The alleged sibling denies it, but the two of them seem to have some history together, though the versions of them we see are from different timelines.
In Havemercy Thom eventually realizes that Rook is his brother, leading to a lot of protest among fans who insist that their UST is undeniable (and it really is...).
In this Percy Jackson and the Olympians sequel series, it is discovered that Jason is Thalia's little brother. And no, not just because they share the same father. They're actual, full-blooded siblings.
Hazel is Nico's sister and Frank turns out to be a descendant of Poseidon, so Percy and Tyson adopt him as their brother.
Leo is related to Sammy Valdez, Hazel's boyfriend from back during World War 2—specifically, he is Sammy's great-grandson.
Heracles and Chrysaor are Jason and Percy's respective half-brothers.note Though it's not difficult to figure it out with the mythological background of the former two in mind, they'd never met before Mark of Athena. They try to kill each other.
Inkmistress: Asra finds out about her half-brother (they have the same divine parent), but unfortunately he died centuries before.
The Jekyll Legacy (by Robert Bloch and Andre Norton): Variant in that the relation is only discovered posthumously — the plot kicks off when Hester Lane, recently arrived in London from Canada (accompanying a girl who was being sent overseas to live with family) discovers that her late father had changed his name before she was born — he was originally Leonard Jekyll, estranged brother of the missing (actually deceased) Dr. Henry Jekyll, making Hester the only blood heir to Dr. Jekyll's estate.
The Kite Runner reveals that Hasaan is Amir's half-brother in a climactic reveal.
The Molly Moon series is full of these. In the course of four books, Molly goes from having no family at all to discovering her mom (Lucy), dad (Primo Cell), her evil uncle (Cornelius), twin brother (Micky), and half-siblings through adoption (Sinclair and Sally Cell)
Moojag and the Auticode Secret: Nema's older brother Monzi went missing ten years ago, around the time of the Surge. Because of his autism, he was taken to Gajoomdom and made to work as a coder with the other auts. He now goes by Moojag, the man who originally invited the protagonists to Gajoomdom.
Valentine Morgenstern is Clary’s biological father.
Jace and Clary end up being siblings... though not before they've sort of fallen in love with each other. Oops...
Once you get to City of Glass, you find out that Jace and Clary aren't related, and that Clary's actual brother is Sebastian.
Amatis Herondale to Luke, more or less, although it's more of the fact that they're estranged siblings and Luke's afraid that she'd blame him for her divorce.
In the first book of The Obsidian Trilogy by Mercedes Lackey and James Mallory, Kellen Tavadon finds that Idalia, the person who nurses him back to health, is his sister (and that their father gave him Laser-Guided Amnesia to avoid bothersome questions from a six-year-old).
Of Fire and Stars: Queen Invasya of Zumorda it turns out is related to Dennaleia (whose maternal grandmother had been Zumordan) through her son who had lived in Havemont, Dennaleia's home country. This probably makes her Dennaleia's great or great-great-grandmother. She learns the queen wants her to be her heir later.
Old Kingdom series: Turns out Sabriel has a half-sister, which is a very good thing considering that neither of her kids is Abhorsen material.
Parzival: Feirefis, Parzival's Moorish long-lost half-brother and ancestor of Prester John is only one of several long-lost relatives in Wolfram von Eschenbach's epic poem, where Everyone Is Related.
The Red Vixen Adventures: In Shadow of Her Sins, Alinadar, who was enslaved by pirates at the age of six, meets an older brother she didn't remember she had.
In Scaramouche, the Heroic Bastard Andre-Louis Moreau gets entangled in a feud with the villainous Marquis de La Tour d'Azyr, who is revealed at the climax to be Andre's biological father. The Marquis is as shocked by the revelation as Andre is; he'd known that the woman he seduced had gotten pregnant, but she'd told him that the child didn't survive being born.
The Baudelaire siblings encounter two of a set of triplets in A Series of Unfortunate Events — the third triplet is a Long Lost Sibling who eventually reunites with his brother and sister.
The titular character in Sir Apropos of Nothing discovers he has a long-lost sister - not quite in time to escape Brother–Sister Incest, but at least to escape marrying her. Unfortunately, he doesn't tell her, which results in her hating him for dumping her so unceremoniously.
In the second Sky Jumpers book, Forbidden Flats, Luke, a traveler who agrees to take a group from White Rock (which includes Hope, Aaren, and Brock) to the town of Heaven's Reach, is discovered to be the brother of Hope's birth mother, making him her uncle.
In Spartan, we have Talos and Brithos. Talos was abandoned by his father when he was a baby, due to his city-state's law that every boy who was born weak or deformed die from exposure. Years later, the two boys meet again and they develop a Sibling Rivalry. They never learn the truth, until the battle at Platea.
Spellbent: Jessie Shimmer finds out she has multiple long lost relatives (her father Ian and her older brother Randall) in Shotgun Sorceress.
Star Trek: In the novelThe Captain's Daughter Hikaru Sulu had sex with a woman he knew as Ling Sui. Even though they were only together one time, it was enough for Ling Sui to become pregnant with a girl she named Demora. Ling Sui - whose real name was Susan Ling - kept the news that Sulu had a daugther with her from him but did identify Sulu as Demora's next of kin in her will. When Ling died of Sakuro's disease Starfleet was informed. Dr. McCoy did a genetic test and confirmed Demora was Sulu's daughter. Sulu decided to turn down the first officer job he was offered on the USS Bozeman in order to raise Demora.
Something like this happens in the Black Fleet Crisis. In one of the two ultimately pointless major plotlines, Luke meets a woman who claims to be close friends with his mother. Apparently a lot of people claim that kind of thing, but he believes this one, since she's Force-sensitive. But she's part of a sect of extremely strict Actual Pacifists and she gives him a bunch of Secret Tests of Character to see if his mother would approve of him, and since Luke readily uses weapons to defend himself and her, he fails all of them. And then it turns out that no, she was lying about knowing his mother and apparently just wanted a chance to moralize on Luke.
During the Dark Nest Trilogy Jacen Solo and Tenel Ka have a daughter they eventually name Allana. They keep Jacen's identity as the father secret even from Han and Leia. As Jacen fell to the dark side of the Force he kidnapped Allana to force Tenel Ka to provide Hapan fleets to him. Han and Leia helped rescue Allana. Back on board the Millenium Falcon the three realize they are related to each other.
Allana Solo: You're Leia Organa Solo. You're Jacen's mommy. He is my daddy." Leia Organa Solo: I know. I am your grandmother. Han Solo: Hi, sweetie; I'm your grandfather.
In the first Survivors book, the street-dog Lucky is reunited with his housepet sister Bella. The two were separated as pups when they were taken into different households.
Talion: Revenant: Marana encounters her long-lost twin sister on a mission, which due to the circumstances drives her insane.
Thora: In the first book, Thora learns that Dottie Greenberg is her Disappeared Dad's mother and her grandmother, and Flossie and Lottie are her great-aunts. She's delighted to finally have an extended family.
In The Vampire Diaries: Midnight it is revealed to Meredith Sulez, by her parents no less, that she has a twin brother who was kidnapped by Klaus when she was just a baby. She also discovers that she is a type of vampire with kitten teeth.
Warrior Cats: Scourge is the half-brother of Firestar through their father Jake. Scourge serves as his sibling's evil foil. They were both born housecats and they both abandoned their owners, but their paths were different. Scourge and Firestar are unaware of their relationship. Scourge ends up taking one of Firestar's lives, which Firestar returns by killing Scourge for trying to kill his (and unknowingly Scourge's) nephew Cloudtail.
