The occurrence of Picocystis salinarum in saline inland waters of East Africa was investigated using a polyphasic approach of small-subunit (SSU) rDNA phylogeny and light microscope observations. Recent studies have found that Picocystis occasionally replaces the dominant cyanobacterium (Arthrospira fusiformis), which is the main food resource of Lesser Flamingos, in soda lakes of Bogoria and Nakuru. This article discusses the consequences of a high abundance (maximum cell numbers of > 3 billion cells l−1) of Picocystis on food chains of African saline waters. During the study, we found a new morphotype of Picocystis characterized by larger cell sizes and absence of lobes in hot springs near Lake Magadi. SSU rRNA genes of Picocystis strains and uncultured field clones collected from Lake Nakuru were subjected to phylogenetic analyses together with other picoplankton from field and culture samples from saline, marine or freshwater. Picocystis salinarum from saline inland waters represents a link between marine and freshwater habitats from both an ecological and a phylogenetic point of view and is therefore of great interest.