Abstract: The 1 010 bp mtDNA ND2 sequences of 125 individuals of Anabas testudineus collected from six basins in South China and Lancang(Mengla, Yunnan Province, China)/Mekong Rive (Tonle Sap Lake, Cambodia) were used to investigate the genetic background in China. The results found 39 variable sites and 12 haplotypes with relatively low genetic diversity (h=0.369, π=0.003 8), which suggests a serious bottleneck effect. Being a peripheral population, the China group had much lower genetic diversity. The pairwise fixation index (F_ST=0.987, P < 0.001) and net genetic distance (0.027 9) between the distinct Cambodia group and China group indicates remarkably high population differentiation. The geology movement and climatic variation might have resulted in geographic isolation and allopatric distribution. Both nucleotide mismatch distribution and neutrality tests show that A.testudineus in China experienced population expansion and the time might be 59.4~41.3 ka BP. No obvious genetic differentiation was found in the populations from six basins in South China. However, remarkable genetic differentiation was found between South China populations and Lancang River population (F_ST =0.775, P < 0.001). Analysis of molecular variance (AMOVA) also reveals that most of genetic variation existed among groups (77.41%), and the deduced differentiation time was approximately 40~28 ka BP, which might be caused by dramatic climatic changes and impassable physical barriers during the last glacial period (32~16 ka BP). The China group and Cambodia group are two management units. As for China group, Han River population should have a priority to be protected for its more genetic variability; Lancang River population also should be protected for its significant population differentiation with the other South China basins and for its lowest genetic diversity.