Ecdysteroids, known as molting hormones, play central roles in the onset of molting, metamorphosis, and reproduction in arthropods. The ecdysteroids stored in eggs also play an important role in embryogenesis. In insects, ecdysteroids are stored as phosphate esters, which are converted to an active form by ecdysteroid-phosphate phosphatase (EPPase). Although EPPase is believed to be widely conserved in the Ecdysozoa, little is known about its expression in clades other than Insecta. In this study, we cloned a putative EPPase gene from a small fresh water crustacean known as a water flea, Daphnia magna Straus (Cladocera: Daphniidae), and examined its expression during embryogenesis. The amino acid sequence of the putative crustacean EPPase cDNA showed high similarity to insect EPPase and human suppressor of T-cell receptor signaling-1. We also found that the D. magna EPPase was highly expressed during early embryogenesis; its expression rapidly decreased 6 h after oviposition. This timing corresponds to the onset of organogenesis in D. magna. The expression of EPPase could not be detected in diapaused eggs. This is the first report of an EPPase from crustaceans, and the results suggest that the function of EPPase is conserved between insects and crustaceans.