The distribution of Daphnia species in tropical Africa is poorly known and understood. Daphnia are assumed rare in tropical regions, but systematic studies covering large areas are sparse. We sampled the active community (live zooplankton) and/or the dormant community (diapausing egg banks in the sediment) of 41 standing water bodies in Kenya in search for Daphnia. Overall the dormant communities yielded 11 species of Daphnia, a species richness more than twice the species richness found in the active communities. Dormant community species diversity better reflects the spatial, and particularly the temporal (multi-annual) variation in environmental conditions available to Daphnia in these tropical standing waters. Hence, we suggest that the dormant community be taken into account when assessing local zooplankton diversity, especially in fluctuating tropical lake ecosystems, where the presence of each local Daphnia species in the active community may be strongly seasonal or erratic. Geographic distribution data from this study are supplemented with previous records of Daphnia in East Africa to provide an overview of the known distribution of Daphnia in Kenya and neighbouring countries. We also present a detailed key for morphological identification of the ephippia of the 11 Daphnia species encountered, complemented with photographs and drawings of diagnostic characters.