We investigated the influence of male flower production, floral synchrony and inter-tree distances on male reproductive success in a miniature seed orchard of Cryptomeria japonica. We used six microsatellite markers to determine the paternity of each seed. In the seed orchard, the average pollen contamination and clonal self-fertilization rates were 38.7 % and 1.7 %, respectively. The level of male reproductive success of constituent clones varied from 0.0 to 15.7 %. Five clones showing the highest male reproductive success contributed ca. 30 % of all analyzed seeds as a pollen donor after excluding contamination by external sources of pollen. The statistical analyses showed that male reproductive success was strongly influenced by male flower production of each clone and, possibly, by their distance to the mother trees. The linear regression which included male flower production and floral synchrony as independent variables, however, accounted for only 14.7 % of variation of male reproductive success, suggesting that other factors such as pollen competition might also influence male reproductive success. Since we found no significant correlation between male reproductive and female reproductive successes, it may be better to equalize male and female reproductive successes independently.