ABSTRACT The Asian elephant ( Elephas maximus ), a crucial flagship and umbrella species in forest ecosystems, possesses significant conservation value. However, it has been categorized as endangered due to several factors, including land use change, human disturbance, and climate change. To evaluate the genetic diversity of Chinese Asian elephant populations and provide a scientific basis for the establishment of the Asian Elephant National Park, microsatellite and mitochondrial DNA analyses were conducted on seven populations distributed across Yunnan Province, China. A total of 121 unique genotypes and five mitochondrial DNA (mtDNA) haplotypes were identified. The results revealed that all populations exhibited varying degrees of inbreeding, with the Mengla population showing the highest inbreeding levels. Significant genetic differentiation was observed between the Mengla and other populations. Interestingly, the Yexianggu population exhibits relatively high genetic diversity despite having undergone a population bottleneck and exhibited significant heterozygote excess. Nevertheless, the overall genetic diversity of Chinese Asian elephants remains relatively low compared to that of populations in other countries. To ensure the long‐term viability of the Nangunhe population, it is imperative to facilitate gene flow between this and other populations. Finally, based on geographic subdivision analysis, we propose that the seven Asian elephant populations should be considered as three conservation management units, namely unit 1 (Nangunhe), unit 2 (Mengla), and unit 3 (Yexianggu, Mengman, Puwen, Kongge, and Menga). This study provides a solid reference for the scientific conservation of the Asian elephant in the future.