Zomboats are sea vessels developed and created by Mechanical Murphy and Mi-Gor, servants of the undead pirate Rabid Jack. They are described as "waterborn cousins of the barrelchests", and appear to be piloted by zombie pirates that have been fused onto them.
During A Clockwork Syringe, the player chases after Murphy and Mi-Gor after destroying the factory on Bloodsplatter Isle, only for them to escape on their own Zomboats, on their way to attack Mos Le'Harmless. The player must then take a nearby unoccupied zomboat, and defeat Mi-Gor's zomboat, Murphy's zomboat and three standard zomboats before they reach Mos Le'Harmless.
The zomboats attack the players own zomboat via their cannons and deal moderate damage. They go down in only two hits from the players own cannon, making them fairly easy to defeat, although they can lower a player's health while a player is fighting Mi-Gor and Murphy, who are considerably tougher.
Zomboats are fought again during Pieces of Hate, where the player must defend Mos Le'Harmless from Rabid Jack's invasion.