Daphnia is a wide spread member of Cladocera living in different aquatic environments ranging from hypersaline swamps to freshwater lakes, lagoons, streams and rivers. To improve our knowledge on the diversity of the genus Daphnia and promote its biogeographical information in Iran, an investigation on the morphology and identification of the Iranian species of the genus was carried out during the spring of 2013 and 2014. The Southern Caspian Sea Basin (SCSB) and Urmia Lake Basin (ULB) Daphnia fauna has been studied based on historical literature records and new collections. Zooplanktons were sampled from 29 randomly chosen localities across ca. 2500 km in the SCSB and ULB basins including both permanent habitats (lakes and reservoirs), and small temporary water bodies (ponds and lagoons), both freshwater and saline. Cladistic analysis of Iranian species of genus Daphnia, based on 64 morphological characters obtained from the literature, confirmed the traditionally basic division of the genus into two subgenera, Daphnia and Ctenodaphnia. This split was supported by enough number of synapomorphies. The relationships between all species within both subgenera were determined clearly. A regional identification key to ten Iranian species of the genus Daphnia was provided.

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