Abstract: A total of 119 individuals of Sillago japonica were collected from six sampling sites (Laizhou, Jiaonan, Zhoushan, Xiamen, Shantou and Beihai). The length of 450 bp NADH dehydrogenase subunit 2 (ND2) gene fragment was amplified and sequenced. No base insertion or deletion mutations occurred and 77 mutation sites were detected, including 30 parsimony informative sites and 28 singleton polymorphic sites. Sixty-one haplotypes were defined in 119 sequences. The average haplotype diversity (H_d) and nucleotide diversity (π) were 0.945 3±0.015 5 and 0.009 718±0.005 445, respectively. The average genetic distance among the six populations was 0.008 3, and the genetic differentiation index F_ST value was less than 0.05, indicating no significant genetic differentiation among the populations. Analysis of molecular variance (AMOVA) shows that genetic variation of S. japonica mainly resided among individuals within populations (99.96%). The neutral tests (Tajima's D and Fu's Fs) were both negative and deviated from the neutral significantly. Besides, the nucleotide mismatches distribution showed a unimodal distribution, indicating that S. japonica had experienced population expansion in history. The estimated expansion time was about 0.12−0.29 million years ago in late Pleistocene.