Forest fragmentation threatens the reproduction of tree species, for which habitats overlap with urban and rural areas. An endangered maple, Acer miyabei f. miyabei, is such a species in northern Japan. We examined the effects of forest fragmentation on seed production and mate diversity and assessed gene flow within and between fragmented forests. We measured the density, viability, and kinship of seeds dispersed around 82 target trees in 21 fragmented forests in rural and urban areas. The dispersed seed density decreased as the size of the target trees and the number of adult trees in each forest decreased. The viable seed proportion also decreased as the number of adult trees in each forest decreased. We did not find any effects on the kinship co-efficient among seeds dispersed around each target tree. The regression line of the pairwise kinship co-efficient of the seeds against the distance had a higher intercept and a more gently declining slope between the forests than within the forests, indicating forest fragmentation altered gene flow patterns. The results suggest reduced seed production due to pollen limitation and changes in the genetic structure of regenerating populations of A. miyabei in fragmented forests.