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- "Crocodiles are responsible for most of the animal-related deaths on Rook, because there's this coming-of-age ritual where young men have to tap a crocodile on the snout with a stick. Reminds me of Thursday nights with my ex-wife."
- — Survival Guide
Crocodiles are found all over the islands, these large reptiles rule over small streams, rivers and swamps. They are primarily found floating just under the surface of the water (usually camouflaged by lilly-pad patches and other floating vegetation) with their eyes and snout partially protruding out of the water. They usually employ their hunting technique near shallow waters and river-shores to be able to catch animals and sometimes humans by surprise. Take caution when approaching, they will wait for the opportune moment and then charge forward towards their victims.
A quick-time event (button mashing) will take place when a crocodile attacks Jason. A button/key will appear on screen to show you what you need to press to avoid death. They can be skinned, but yield nothing noteworthy besides Leather, which can be sold for $10.
A Brown crocodile also appears in the mission Down in the Docks. This is the first time (not including free-roam) that the crocodile is introduced in the game.
- Crocodiles never leave the water unless it is to lunge at the player, but when an animal or NPC is attacked, they get pulled into the water with minimal struggle.
- A rare Albino Crocodile exists in a remote swamp on the Southern Island. This unique Crocodile is encountered in a Path of the Hunter mission where you are required to kill it with a machete. Physically the Albino Crocodile resembles a Saltwater Crocodile with the only difference being that it has white skin and more health than its green-skinned cousins.
- There is a common scripted event where a civilian will wander into a river or lake for seemingly no reason and get attacked and killed by a crocodile. This will happen virtually every time a civilian get next to or in the water and can be useful for finding the location of crocodiles.
- Crocodiles cannot be tagged with Jasons camera. This is probably so that the players don't use advantage of it and avoid crocodiles altogether.
- In Far Cry 3 map editor, if a crocodile is placed on land, it will use the animation as if it were swimming. This is probably because Ubisoft never intended the crocodile to leave the water.