In order to understand the mystery of life, it is of importance to accumulate genomic information in various organisms because the whole genomic data encodes the command for all of them. Here we report a draft genome of the sea urchin, Hemincentrotus pulcherrimus, because this species has long history as the target of developmental and cell biology in the East Asia. The genome of H.p. was assembled into 16,251 scaffold sequences with N50 length of 143k bp and approximately 25,000 genes were identified in the genome. The size of genome and sequencing coverage were estimated to be around 800M bp and 100x, respectively.