The Japanese captive population of Crested Ibis (Nipponia nippon) has rapidly increased, and reintroduction programs were initiated on Sado Island in 2008. The Japanese captive population, however, was founded by only 5 individuals originating from the Chinese captive population. Because efforts were directed toward preserving genetic diversity in the captive population, it was appropriate to consider genetic diversity in the reintroduced population to evaluate its potential to survive in the wild, where environmental changes are more significant than in captivity. The purpose of this study was to determine the number of individuals to release in the future to preserve genetic diversity of the reintroduced population. We simulated the probability that the reintroduced population after 50 years would retain a rare allele existing in the captive population, based on demographic parameters obtained from either the Japanese captive or reintroduced populations, or Chinese wild populations. As a result, the 10–15 individuals currently released in the annual reintroduction would be the number needed to be released each year over 50 years to retain the rare allele with a frequency in the captive population of 0.05 with a >90% probability. Therefore, the current reintroduction program seems reasonable and should be continued.