Cladoceran species have been widely used for ecotoxicity assessments of chemicals and environmental contamination. National Instite for Environmental Studies, Japan (NIES) has maintained several cladoceran species (e.g., Daphnia magna, Ceriodaphnia dubia) for more than 30 years, and has provided testing laboratories with these species. In this project, the genomes of these species was sequenced to provide the information useful for phylogenetic and ecotoxicological analyses.