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The introgression from genetically modified soybean (Glycine max (L)) to wild soybean (Glycine soja Sieb. et Zucc.) could be threat the genetic diversity of wild soybean. Flowering synchrony is essential to the occurrence of outcrossing, but the flowering phenology of wild soybean is less well researched than that of cultivated soybean. We developed models to predict flowering initiation of wild soybean, based on the flowering initiation dates of wild soybean five accessions from different latitudes (31.4°N to 42.6°N) in growth chambers in which temperature and day length varied. Our proposed models predicted the flowering initiation date of wild soybean in the natural habitat well; the averaged difference from observed date in 5 areas was -1.8 days (-8 to +5). In the long day condition, there was a clear latitudinal cline of photoperiodic sensitivity throughout Japan. Accessions in southern part of Japan archipelago required higher temperature even under the short-day conditions and northern accessions were less-sensitive to long-day conditions. Our result showed the possibility of predicting the flowering initiation of wild soybean, corresponding to latitudes.