The medaka Oryzias latipes is a small egg-laying freshwater teleost, and has become an excellent model system for ecotoxicology, developmental genetics, genomics and evolutionary biology studies. A high-quality draft genome sequence (700 Mb) of the medaka inbred strain, Hd-rR, has now been completed. In this review, we present an overview of the medaka genome project and describe the substantial genomic resources and genome browsers through which researchers can now freely access these resources. We also present specific findings that have been obtained using these tools, such as sex chromosome differentiation, gene prediction and gene evolution.