Allozyme diversity was examined in 30 populations of the maritime perennial plant Hedyotis strigulosa var. parviflora, which is distributed from subtropical islands to the central mainland of Japan. Genetic diversity within populations tended to be larger in southern island populations than in northern mainland populations. In the southern part of the distribution, the population size is generally large and populations are distributed more continuously than in the northern area, resulting in the larger effective size of southern populations as a whole. These factors play a major role in maintaining greater genetic diversity in the southern populations. By contrast, genetic diversity in the northern populations is very low, probably resulting from bottlenecks of population establishments during recolonization from refugial area to the northern areas. Geographically close populations were located near each other in the multidimensional scaling and the phenogram based on genetic distances, suggesting that gene flow among remote populations is rather limited. The pattern of genetic diversity in H. strigulosa var. parviflora is likely caused by the distribution expansion of the species; in the last glacier era, the species was restricted to the southern area; its advance to the northern area is relatively recent. Another variety endemic only to the Daito Islands, H. strigulosa var. luxurians, has lower genetic diversity than H. strigulosa var. parviflora and has genetically diverged from H. strigulosa var. parviflora. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 679–688.