We studied the genetic differentiation in budburst timing among Fagus crenata populations along spatial gradients in late frost timing in the Hakkoda Mountains, northern Japan, by focusing on last fatal frost day and topography. For budburst timing, we analyzed interpopulation variations in habitats, genetic variations in a nursery, and the relationships between these variations and environmental conditions in the habitats. Analyses of interpopulation variation showed that the day and the temperature sum of budburst positively correlated with the last fatal frost day in the habitats. Analyses of genetic variation showed significant genetic variations among provenances and families for both traits. For all provenances, the heritability for these traits were 0.7–0.8. The genetic variations were significantly associated with variations in the last fatal frost day among the provenances, suggesting that natural selection due to late fatal frost causes genetic differentiation in the traits along the spatial gradient in late frost timing. These results demonstrate that late frost is a key factor driving genetic differentiation of leaf-out phenology within a regional tree population.