The red panda (Ailurus fulgens) is an endangered species that is indigenous to Asia. This species is currently under serious threat due to habitat loss and fragmentation as well as to human activities. In China, red pandas have been raised in zoos for 60 years, and more than 400 individuals live in approximately 55 zoos today. Therefore, the genetic diversity and population genetic structure of captive red pandas must be understood. The genetic diversity and population genetic structure of 116 captive red pandas from 11 captive populations in China were investigated on the basis of 19 microsatellite loci. Our results revealed a high genetic diversity among the populations, with mean allelic richness varying from 3.505 ± 1.033 (Beijing) to 4.026 ± 1.219 (Mianning), and expected heterozygosity varying from 0.631 ± 0.225 (Huangshan) to 0.782 ± 0.171 (Wenling). In particular, significant deviation from the Hardy–Weinberg equilibrium was found in populations from Fuzhou and Jiangsu. The genetic differentiation index across all populations was 0.055, indicating significant genetic differentiation among the 11 populations. The 11 populations investigated were categorized into three genetic clusters through a microsatellite-based Bayesian clustering analysis, and they were consistent with the clustering results of wild populations. Overall, the genetic diversity among captive red pandas is as high as that of the wild population. Thus, to avoid inbreeding and maintain high genetic diversity among captive red pandas, more attention should be paid to developing a suitable, scientific breeding program, rather than introducing additional wild individuals into captivity.