Morphological variation of the chrysophyte stomatocyst found in surface sediments of a small, shallow lake in the Guineo-Congolian rainforest in eastern Cameroon, is described, illustrated and discussed. Neither living cells nor scales of chrysophytes were observed in the lake. The stomatocyst cannot be assigned to any known cyst and is described as new to science (stomatocyst #49) using International Statospore Working Group (ISWG) guidelines. This is the third report of stomatocysts in Africa, and the second from the tropical part of this continent. Some basic ecological information on the sampling site is provided and compared with similar data from other sampling sites of chrysophytes in Africa.