Callicarpa subpubescens is endemic to the oceanic Ogasawara Islands, and multiple ecotypes have been suggested to exist within southern part of this group, the Hahajima Islands, each associated with unique localized habitats. We determined the habitat characteristics of each ecotype, the presence or absence of pre- and post-mating isolation, the amount of gene flow among ecotypes in adult trees and naturally pollinated seeds using EST-SSR markers, and discussed how ecotypes are maintained in this species. There were four ecotypes in the Hahajima Islands, one of which presumed to be derived from hybridization of the remaining two ecotypes. The spatial distribution and habitat of each ecotype showed distribution which have depended on the suitable environment for each ecotype, i.e. local adaptation. The leaf morphology and size distribution of each ecotype also indicated the appropriate forms for each habitat. Flowering times more or less overlap among the ecotypes, indicating that pre-mating isolation is not perfect. Artificial cross-pollination showed that no post-mating isolation exists between ecotypes. Hybridization rates in adult trees and naturally pollinated seeds were 37.2% and 26.4%, respectively, and most of the hybrids were backcrosses and few F1. The hybridization rates of each ecotype and paternal correlation indicated that the flowering synchrony and spatial distribution of ecotypes contributed to hybridization among ecotypes. The reversion to the original ecotype which adapted to the environment through backcrossing would contribute to the maintenance of the ecotypes.