The mechanism of local adaptation through flowering time is one of the important factors to understand the local adaptation in plant species. Improving the recent sequencing technology enables to detect causable candidates for various kinds of phenotypes with genome-wide association study (GWAS). L. japonicus is a legume model plant and distributed in whole range of Japan. The archipelago lies in the wide range of latitude and harbors various environments including high mountain ranges and coastline. Based on previous studies, this plant exhibits wide variation of flowering time depends on habitat’s latitude. In this study, GWA analyses were conducted with flowering time phenotype and environmental factors of each population’s collection sites. Considering the overlaps of the detected genes, several candidate loci for local adaptation through flowering time were found.