A Special Edition was created in 2009. This version contains hand-drawn, updated graphics, more elaborate backgrounds, a remastered musical score and a hint system. Verb commands and items are no longer in standard display at the bottom of the screen, but appear in pop-up screens. This version also has voice dialogue, recorded by many series' veterans (such as Dominic Armato as Guybrush and Earl Boen as LeChuck). It is possible to toggle between the new graphics and the original 90s-style graphics while playing. This version also completely omits the infamous 'tree stump' joke that confused players back in 1990.
Regardless of the version of the game (the 16-color version, the 256-color version or the Special Edition), after Guybrush ends up on Monkey Island, there is a choice he can make that will slightly affect the ending of the game. To get the canon ending, Guybrush has to use the 'primitive art' on one of the mountains to throw a rock on a banana tree on the beach (he should NOT hit his ship). When Guybrush returns with the root extract to LeChuck's ship, the ship is gone and only ghost crewman Bob is there. Guybrush' crew members then show up to take him back to the ship and return to Melée Island. After defeating LeChuck, Guybrush realizes that he completely forgot about Herman Toothrot. Herman can be seen standing on a beach on Monkey Island, hoping that Guybrush didn't leave him behind. An alternative ending is obtained if Guybrush uses the primitive art to accidentally hit and sink his own ship the Sea Monkey. If this happens, Herman Toothrot will appear in the cave. It turns out he has a ship, but couldn't use it, since according to the rules, "if you're stranded, you got to be rescued"; he'll lend Guybrush the ship if he promises to rescue him with it. After defeating LeChuck, Guybrush wishes that his crew could have seen this. We then see Meathook, Otis and Carla locked inside the hut in the Cannibal village. Otis has suspicions that Guybrush was responsible for sinking their ship; Carla says that they will have a chat with him as soon as they get off the island (after they have escaped from the hut).
Newer versions have verbs and inventory like the newer graphic adventures. This includes larger verbs and pictures for the inventory.
There are two versions of the game. The original one, with 16-color graphics and text for verbs and inventory. A newer version was later created that uses the 256-color palatte (richer, more varying colors) and has graphic pictures instead of words for the inventory. Less-used verbs were also removed from the verb list. Additionally, the CD version of the 256 version features new music tracks.
In the original PC floppy versions, there was a joke in the woods; when you tried to look in the tree stump, a message saying something along the lines of "insert disk 21", which would be followed by other requests for ridiculously-numbered disks. This gag was later removed from all CD versions.