Botrylloides simodensis, belonging to the family Botryllidae, is a common species on the rocky shore around Shimoda. Since this species was first reported in 1981, it has been noticed that some B. simodensis colonies have distinctly different ground colors and color patterns from colonies including type specimens (holotype and all of paratypes) of B. simodensis. However, as there is no remarkable difference among them in morphology other than the colonial colors and color patterns, they have been considered to belong to the same species. In the present work, colonies of B. simodensis sensu lato were divided into three groups, two major and one minor, based on their color-morphs and periods of sexual reproduction. In one of the major groups, B. simodensis sensu strict, the period of sexual reproduction was limited from July to September, as shown in the original description. The other major group engaged in sexual reproduction for much longer than the former group, and they frequently made clusters of vascular vessels and underwent vascular budding. Therefore, the group with the long period of sexual reproduction was described as a new species of the genus Botrylloides here. In addition, phylogenetic analysis based on mtDNA sequences of these groups indicated that each group had a peculiar sequence, and that they were genetically separated.