In 2017 we started a project to analyze the ecology and phylogeny of western Pacific echinoids. As the first step, we are establishing methods to infer their phylogenetic relationships using molecular data; we developed effective methods to obtain complete mitochondrial DNA sequences, and determined their effectiveness in phylogenetic analysis. We have also been gathering data concerning the ecology and systematics of Japanese extant echinoids, which arguably has among the highest genus-level diversities in the West Pacific or perhaps even in the world. We have collected 58 species from middle and southern Japan representing 48 genera. In the next year, we will collect sea urchins from northern Japan, and within 2 years we will finish collecting data on ecology and systematics of Japanese echinoids, and provide a set of standardized data that will be useful for many researchers studying western Pacific echinoids. At that time, we will start comparative analyses of echinoid faunas distributed in the western Pacific.