In old times, mapmaking was a fairly imprecise task, due to the lack of advanced technology for exploration purposes. So, to fill great blank areas on the maps, mapmakers used to include textual and/or graphic warnings of the dangers of going into uncharted territory. Such warnings took the form of sea serpents, dragons, cannibals and many other mythical and, sometimes, even real creatures. The actual line "Here There Be Dragons" has been found only once, on the 16th-century Lenox Globe — but is too cool to give up.
This tendency is explored in fiction with two usual objectives. The first and more obvious is to show that the map is very ancient or simply medieval. Depending on the setting, the map may be contemporary, but displayed in an outdated manner because that's how things still are made.
The other use of this trope is to avoid showing the viewer a dull and realistic map. This is mostly used in video games, to give the world map a more enjoyable presentation.
In fiction, many maps don't just warn its readers of the great perils on their way, but sometimes also contain other pieces of information, such as the location of cities and landmarks, pointed by stylistically out-of-scale drawings.
Because Everything's Better In Latin, also sometimes seen as its original spelling, Hic sunt dracones.
Do not mistake this with Here There Were Dragons, which is about the existance of magic (and even dragons) sometime in the past of the setting of a fictional work. Also not to be confused with the fantasy movie review show by Nash of TGWTG.
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Anime and Manga
Skypiea's map in One Piece had several symbols, including a ziggurat (marking the position of Eldorado) and some devilish creature roaming through the land.
How to Train Your Dragon has a map with, wouldn't you know it, dragons. This is meant literally, as it signals the dragon's nest.
In Pirates of the Caribbean, during Barbossa and Jack's swordfight, Barbossa gloats over Jack having gotten in way over his head (by, y'know, engaging in single combat with an immortal), taunting him by saying "You're off the edge of the map, matey. Here there be monsters!"
The credits of Cars 2 did this with submarines, which appear to serve as stand-ins for whales.
The map in The Hobbit depicts the location of Smaug's Lair with the drawing of a dragon, and spiders on the Dark Forest. It also has an arrow pointing off the edge of the plotted area, noting that to the north lies a terrible wasteland "whence came the Great Wyrms".
Parodied in Discworld, where tourists' maps of Anhk-Morpork are labelled "Here Be Dragons" to mark the location of the Sunshine Sanctuary For Sick Dragons, a veterinary hospital. The same phrase appears over the actual Sanctuary's entrance as grafitti.
Elsewhere in Discworld we're told that cartographers sometimes got so carried away with drawing sea monsters that they forgot to put the boring countries and so on in at all.
In a rather wonderful moment in The High Crusade, the narrator (a Medieval monk) criticizes a technologically advanced alien map. Sure, it might be accurate, but its lack of dragons, mermaids, sea serpents and such ornamentation shows a poverty of cultural imagination and depth.
Discussed in the Lord Peter Wimsey story "The Learned Adventure of the Dragon's Head". One of the things that arouses Lord Peter's suspicion of the villain is that he claims to have seen "hic dracones" on the maps in a mediaeval book. Lord Peter, being an actual book collector, knows how unlikely this is.
Throughout the Star Wars Expanded Universe novel CrosscurrentThe Hero Jaden Korr uses "There be Dragons...", when thinking about his doubts about himself, the force, and everything.
There is a fairly obscure book series by James A. Owen that is all about this trope, and cartography in general. The title of the first book is the name of this trope. The series name is The Chronicles of the Imaginarium Geographica, and it's about The Multiverse of written fiction in one alternate dimension.
Here Be Dragons is a science fiction novel whose main character keeps a print of a centuries old map which seems to be a cross between the Lenox globe and the Carta Marina.
The maps seen at the beginning of T.A. Barron's The Lost Years of Merlin series feature this, with various creatures depicted in the series, such as kreelixes.
Hitherby Dragons takes this trope as its main theme (and indeed, its very title): in the same way as map-makers didn't know what the world was like physically, and thus drew dragons to represent the unknown, Hitherby's characters don't know the answers to big philosophical questions, but still try to find them, in their own ways.
Non-fiction French book Tour du monde des terres françaises oubliées ("Circumnavigation of Forgotten French Lands", which is about the obscure tiny isolated islands owned by France: Clipperton, Chesterfield, French Southern and Antarctic Lands, etc) comes with a map indicating the location of the various lands mentioned in the book. The map is decorated with various fantastic creatures.
Live Action TV
On Head of the Class Billy Connolly referenced this in the context of showing off the new world maps the school bought - he said the other ones were so old they had "Here dragons be" indicators.
In Doctor Who, the opening of "The Last of the Time Lords" reveals that the planet Earth and our entire solar system was declared strictly off-limits by the rest of the universe, after Master seized control of the planet during "The YearThat Never Was".
Discussed by Lorne Malvo in the pilot of Fargo while attempting to warn off an inquisitive traffic cop, suggesting that poking into his affairs will not end any better than attempting to chart such seas.
Wario Land: The Shake Dimension had one of these maps◊. Note the mermaid, sea serpent and octopus-like creature in various points on the map and the old-fashioned compass (itself something many of these maps also contain).
Fanciful illustrations can be found on the in-game Arcanum world map, in keeping with the setting. Most of these pictures are of animals not found in that locale, or at all, but at least one provides a little hint of what you'll find there.
Eternal Darkness had the actual line "Here Be Dragons" on a globe in the observatory.
An Easter Egg in Grand Theft Auto: Chinatown Wars references the trope: swim out to any of the four corner of the game map, and you'll find a sign with old-script telling you that "Here Be Dragons", which is as good a Hand Wave as any for why you can't get away from Liberty City.
In Return to Ravenhearst, the schoolroom where Rose's daughters were indoctrinated by Charles Dalimar has a crude outline of England and Wales on its wall map, in which everything else is blank and marked "unknown". No actual monsters are depicted, but the creepiness of the script implies that horrible things lurk beyond the borders.
In Risen while there's no mention on the map, if you go out too far into the sea, a giant sea monster bursts out of the water and eats you. Humorously, you'll wake up on the beach a bit later without any harm. Observe here.
In the intro to the original Colonization your colony ship sails across one of these, encountering various sea serpents and anthropomorphic storm clouds as it goes.
Played with in Monkey Island 2: LeChuck's Revenge where the map shows the three main islands as well as a bunch of superfluous symbols in the blank areas. Clicking anywhere near them makes Captain Dread exclaim "We can't go there, mon. That's the forbidden triangle", or any other shape, including elliptic hyperboloid.
Miner VGA will display "Here Be Dragons" if you try to go off the left or right edges of the playable area. Yes, even if you do it underground.
The Age of Empires II expansion included a Viking mission where you had to get to the New World. To avoid the simple idea of sailing around Greenland, there was some odd water to the South that destroyed your ships. After conquering some of Greenland, the area was revealed by the computer, showing the shape of a dragon on the minimap.
Freeman's Mind: In one episode Gordon Freeman encounters an utterly useless map and mocks it by using this trope:
Freeman: Oh sweet a map! Ok so where am I ... which way's North? Maintenance shaft ... that .. could be anything; half this building is a maintenance shaft. What's that big room, is that where the monster is? What about this radiation pit? High voltage ... that has to be where I came from. But what the hell is with these distances then? Why are parts of this map grayed out? Is it haunted? WHY IS THERE NO EXIT ON THIS MAP? Is there a landmark ...? This map is bullshit; I'm gonna find my own way out of here. That map has to be bogus; it only lists one area as being dangerous. It needs to have, like, 30. You could even write "Here be dragons" on it, and it would almost be more accurate than nothing at all.
In a sense the Universe runs in this trope. It's so immense that, despite we've send probes to all the planets of the Solar System and the extensive surveys done with telescopes, can be considered uncharted (to give one example in our Solar System, it's still unclear if the Oort cloud exists or not). We may know many stars have planets, but until the day we can go to that planets (if that day arrives) it's impossible to know what could be waiting for us there. Same to a larger extent for the other hundreds of billions of stars that compose our galaxy, to say nothing of other galaxies.
Other astronomical example could be the Zone of Avoidance of the Milky Way, at least until became possible to study that area of the sky with in other wavelengths (infrared, radio, X-Ray...) that weren't so affected by the interstellar dust as the visible light.
The best example, however, is what lies beyond the edge of the observable universe, at 46 billion l.y. from here note http://en.wikipedia.org/wiki/Observable_universe not 13.7 billion l.y. as one could think. At most be can guess it's very likely there's (far) more Universe beyond that limit and that, if the Cosmological principle holds outside too we'd find the same structures than in our vicinity (galaxies, clusters of galaxies, etc) if we could look so far away, but that's all. There's no way to know if the Universe is finite or infinite, nor what really lies beyond that edge and maybe that will never be known.
An example where someone went there and still said Here There Be Dragons: Marco Polo describes some "dragons" in his accounts of traveling in Asia. They were possibly monitor lizards or Chinese alligators.