We generated RNA-seq data for the water flea Daphnia mitsukuri at five developmental stages, including the embryo and representative post-embryonic stages in the life cycle. Embryos showed a large number of unique and highly expressed genes, mainly related to DNA replication, differentiation, morphogenesis and the Hippo signaling pathway. Post-embryonic stages showed an enrichment of transcripts for genes involved in chemosensory perception, visual perception, cuticle formation and antioxidative defense. These specific highly expressed transcripts at post-embryonic stages are essential to help Daphnia to respond to current or likely environmental stresses. Our data provide a high-resolution view of transcriptome dynamics throughout development of Daphnia, a model organism for ecology and evolution.