We collected Chinese cobras (Naja atra) from one island (Dinghai) and four mainland (Huangshan, Lishui, Quanzhou, and Baise) populations in southeastern China, and used sequence data derived from the ND2 (1032 bp) and cytochrome b (1117 bp) genes and molecular variance estimates to investigate the population genetic structure of the species. Our sequence data show that: (1) the three eastern (Dinghai, Huangshan, and Lishui) populations are genetically segregated from the two southern (Quanzhou and Baise) populations; (2) the Quanzhou and Baise populations consist of two well-defined subclades, suggesting that the two populations have been well differentiated; (3) N. atra from the Huangshan population do not differ from those from the Lishui population, and lineage sorting in the northeastern part of the cobra’s distributional range has not yet been completed because of the young age of Zhoushan Islands. The three eastern populations, the Quanzhou population, and the Baise population should be regarded as different management units (MUs). For these MUs, we suggest that in-situ protection measures should be taken because of their genetic uniqueness. Re-introductions or translocations are required to protect or re-establish natural populations of N. atra, but great care should be taken to enhance or retain local genetic variation.