In Reef Encounter the aim is to grow the largest and strongest corals on the reef and then to feed these to your parrotfish in the brief time available. Points are awarded at the end of the game for the number and type of polyps that your parrotfish has consumed.
Each turn new coral larvae drift into the game. Larva cubes allow players to play their polyp tiles onto the boards and create new and larger corals. Shrimps will then colonize these corals and protect the corals from attack.
A coral consists of one or more connected polyp tiles. Corals that are two or more polyps in size may attack other weaker types of coral. Polyps from a defeated coral can be recycled as new polyps or alternatively used to obtain alga cylinders or larva cubes.
It is the alga cylinders, which will strengthen some types of corals relative to the other types. An alga cylinder can also fix the hierarchy between two particular types of coral for the remainder of the game.
Reef Encounter will usually end once the hierarchy of all the corals is established or once one player's parrotfish has consumed four corals.