Variation of female and male strobilus production among clones over 4 consecutive years was estimated, and genetic variance, heritability, and genetic correlation in strobilus production were investigated in the second-generation seed orchard of Pinus thunbergii. This seed orchard was created with grafts selected according to the volume growth of their offspring. The production of female strobili continued to increase, whereas the production of male strobili fluctuated throughout the investigated period. The number of female strobili was highest in rich cone years, but the production of male strobili was not the same in rich or poor years. The maleness index showed a balance between female and male parents that occurred when male strobilus production was in rich or poor years. The parental balance curve for female strobilus production was closer to the expectation (i.e., more equal contribution) than that for male strobilus production in all years. The analysis of variance revealed significant differences among clones in female and male strobilus production over the four-year period. The narrow-sense heritability was higher in male strobilus production than female strobilus, implying that male strobilus production was under genetic control. The Pearson’s correlation was positive and mostly significant, indicating that female strobilus production was reflected in male strobilus production. The effective parent number was lowest in moderate and good years for cone production. The loss of gene diversity in seed crops was lower than expected based on clonal fertility variation.
