Along with range shifts created by climate changes at the margins of a species’ range may undergo significant evolutionary processes associated with isolation and secondary contacts. We investigate divergence and migration in two related species, Rubus grayanus, and R. palmatus, whose northern and southern range limits, respectively, are overlapping on the Yakushima Island. We studied four populations; two allopatric populations, one in each species and two parapatric populations on Yakushima Island. Isolation-with-Migration analyses with 12 putatively functional genes revealed that the two populations of R. palmatus diverged before the Last Glacial Maximum (LGM) and have been isolated and persisted since then, while the R. grayanus populations diverged very recently and likely represent young outposts of a northbound range shift. Significant gene flow was only detected between the parapatric populations of R. palmatus and R. grayanus on Yakushima Island. These results suggest that each species responded to climate change in different rates, and it caused secondary contacts and introgression, which could provide genetic variation at the margins of the species’ ranges.