The absence of phylogeographical pattern in Japanese coastal plants has been empirically detected primarily due to the frequent gene flow (seed dispersal) mediated by sea current. However, wild radish (Raphanus sativus L.) as a typical coastal plant in Japan harbors the considerable phenological and phenotypic variations among the habitat localities, e.g., flowering time and leaf morphology. Thereby, wild radish would exhibit phylogeographical pattern that congruent with their phenological and phenotypic differentiation. To verify this hypothesis, comprehensive investigations of the phylogeographical pattern and demographic history of wild radish were conducted based on SSR analysis and DNA sequences of the 14 nuclear loci. Both of the Bayesian clustering analysis based on these two dataset showed marked genetic differentiation between the Ryukyu Islands and mainland Japan populations. In addition, demographic histories (divergence time and migration rate) in these two clusters (Ryukyu Islands and mainland Japan groups) were estimated using the isolation-with-migration model analysis (This part will be discussed hereafter). Our results indicated that geographical isolation may profoundly impact phylogeographical patterns and demographic history.