Background Seed stand is one of the important seed sources that is essential for global seed production programs. The primary objective of seed stands is to produce seeds as fast as possible. Characteristics of seed stand seeds depend mainly on stand quality, fertility variation and mating system. Individual fertility is an ability to produce progeny to next generation. Prediction of fertility variation is useful for seed production, genetic resources management and gene conservation. In this study, we report how to estimate fertility variation and gene diversity, and discuss its effect on the management of natural stands of Taurus cedar. Results Fertility variation and gene diversity were estimated based on the differences of strobilus production in female and male parents from three seed stands of Taurus cedar. A total of 50 trees were randomly chosen from each seed stand, and the female and male strobili were counted for three consecutive years. The coefficients of variation for female and male strobilus production were subjected to estimation female and male fertility variation. The total fertility variation (Ψ) was then estimated from the female and male fertility variation. The effective number of parents ( Np ) was calculated based on the Ψ. The mean of female strobili ranged from 31 to 150, and that of male strobili ranged between 77 and 828. The Ψ in a good crop year was smaller than in a poor year and the Np varied from 34.7 to 44.2. The Ψ was improved and the Np was increased when strobilus productions were pooled across three years or populations. The equal cone harvest could mitigate the fertility variation among individuals but caused loss of seed production. Conclusions The effective number of parents could estimate gene diversity of seeds from natural stands, which was based on the function of correlated fertility variation between female and male parents. Mixing seeds from different years could improve the fertility variation among individuals and increase the gene diversity of seeds. However, a balancing between the effective number of parents and the number of mixed years or populations should be carefully considered for maintaining the gene diversity.