We studied habitats of sea urchin species in Shirkawa Bay in Yamaguchi City, Yamaguchi Prefecture, during the period from June 2005 to June 2007. Nine species were identified from Shirikawa Bay, which included 6 families. Several hundreds of Scaphechinus mirabilis appeared in a sandy beach in only early spring, while some regular sea urchin species, the mature Hemicentrotus pulcherrimus and the smaller Anthocidaris crassispine than ones in a shore out of the bay, were found often under the rocks in a shore in the bay through these survey periods. Additionally, Pseudocentrotus depressus were always found in the subtidal zone in a shore in/out of the bay. In a muddy beach, the only mature Temnopleurus toreumaticus inhabited. These results suggested that each sea urchin species in Shirikawa Bay segregates the own habitat and that S. mirabilis may change their habitats for spawning. We also investigated the breeding seasons of H. pulcherrimus and T. toreumaticus in this area by chemical induction of spawning. H. pulcherrimus spawned mature gametes from the middle of December to the middle of April and T. toreumaticus did from June to the middle of November. These results indicate the possibility that the provision of mature gametes by these species for a whole year contributes to the developmental biology with sea urchins in this area.