Lake Tanganyika, the second oldest lake in the world, is home to some of the largest and most phenotypically, genetically, and ecologically diverse freshwater assemblages. While the evolutionary processes responsible for generating its extraordinary richness are well understood across various animal groups, little is known about the diatom species richness, turnover patterns, and their drivers. Here, we explored species richness of the diatom genus Diploneis from Lake Tanganyika and surrounding regions by using morphological and molecular information. Both datasets suggested the presence of twenty-five new Diploneis species, each not related to any known Diploneis species so far. The multi-locus phylogeny indicates a monophyletic group of twenty-one Diploneis species from Lake Tanganyika, suggesting potential intralacustrine diversification possibly triggered by certain historical contingencies. This is supported by the small genetic distances and the presence of unique silica ornamentations on the valve face exterior, to date only known to occur on the Baikal endemic Diploneis implicatus. The discovery of such a high richness of Diploneis species in Lake Tanganyika and the presence of a unique morphological character points to a potential adaptive radiation - a mechanism yet to be confirmed.