Genotypes at five microsatellite loci of 361 Cercidiphyllum japonicum seeds and identity numbers of their seed-parents in a population distributed over about 80 ha along a stream within Iwanazawa Forest Reserve (43°13′N, 142°34′E), University of Tokyo Hokkaido Forest, in central Hokkaido, Japan. Based on this and another data (https://doi.org/10.5061/dryad.zcrjdfnb7), pattern of gene dispersal via pollen in this population was estimated by neighborhood model approach and Two generation analysis (TwoGener). These data set can be reused for review of the study and would be useful for comparison with other studies on gene dispersal of tree species.