Detailed knowledge of the molecular mechanisms of controlling flowering time will facilitate understanding the adaptation mechanism in cultivated rice and enable breeders to design appropriate genotypes for distinct preferences. Previous studies showed that PhyB suppress flowering in long day (LD) conditions, however, how the genetic variation of PhyB is associated with flowering time in different varieties in rice remains unknown. In this study, we sequenced 78 cultivated rice varieties (34 indica varieties and 44 japonica varieties) and 47 wild relatives of rice for PhyB. We obtained the following results: 28 haplotypes were detected among the 125 accessions, and there were two prevalent haplotypes which mainly existed in cultivated rice. The Network indicated that the cultivated rice could be divided into two groups (group A and group B), in which, group A included all indica individuals and 4 japonica individuals, and group B included the rest of japonica individuals. Further geographical analysis showed that group A and group B had distinct geographic distribution pattern, and the flowering time between group A and group B were significantly different. In addition, the genetic diversity result showed that wild rice population harbored higher genetic diversity than did the two cultivated subspecies (indica and japonica). Thus, we inferred that the two prevalent haplotypes existed in two cultivated subspecies are associated with regional adaptability. PhyB had obvious domestication signals in cultivated rice. It evolved specific alleles to adapt the day time suitable for flowering of rice varieties in different regions.