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Castanopsis (Fagaceae) is a plant genus that includes dominant tree species in the broadleaved evergreen forests of Japan. In this study, we investigated the genetic diversity and genetic structure of 76 natural populations of C. sieboldii and C. cuspidata, using variations in chloroplast DNA (cpDNA) sequences and chloroplast microsatellites (cpSSR) to elucidate the phylogeographic patterns reflected by seed flow. Most chloroplast haplotypes were shared between the two species on the main islands, although biparentally inherited microsatellite (nSSR) analyses showed a species-specific pattern in the previous study. The current patterns of haplotype sharing of cpDNA suggest the retention of an ancestral polymorphism that existed in Castanopsis before the two species split or historical introgression in the refugia during the glacial periods. Haplotype network was defined by three groups: Taiwan, southern parts of the Ryukyu Islands, and the central parts of the Ryukyu Islands to the main islands. The observed north-south genetic differentiation in cpDNA on the Ryukyu Islands was not detected by previous nSSR analyses. These results suggest that the lower levels of seed-mediated gene flow between the islands resulted in clear genetic differentiation of cpDNA on the Ryukyu Islands. Moreover, the cpSSR analysis indicated east-west genetic differentiation on the main islands, a pattern found in previous nSSR analyses of Castanopsis and several plant and animal species inhabiting Castanopsis forests in Japan, suggesting the existence of eastern refugia in the last glacial period. Our cpSSR investigation and their higher intraspecific variation provide a useful phylogeographic tool for these species. [ABSTRACT FROM AUTHOR]