Abstract: To investigate the genetic diversity and structure of Phascolosoma esculenta wild populations in the coastal zone of South-Eastern China, the mitochondrial cytochrome oxidase subunit Ⅰ (COⅠ) genes as molecular markers were amplified, sequenced and analyzed from 80 organisms sampled in four areas Xiangshan (XS), Wenling (WL), Ningde (ND) and Zhanjiang (ZJ). The results showed that 815 base pair (bp) fragment was consisted of A, T, C and G base with 29.8%, 31.0%, 22.6% and 16.6%, respectively, indicating a greater preference for A and T base because the A+T content (60.8%) was higher than that of G+C (39.2%). Besides, twenty-nine polymorphic sites and haplotypes were identified in all the sequences. Total haplotype diversity (H_d), nucleotide diversity (P_i) and the average number of nucleotide differences (K) were 0.932, 0.0036 and 2.8902, respectively. A shallow topology of haplotype neighbor-joining (NJ) tree with simple topological structure showed no phylogeographic structure among four populations. Genetic distance within and between P. esulenta populations were 0.0027—0.0040 and 0.0032—0.0040, respectively. Genetic fixation index (F_st) and analysis of molecular variance (AMOVA) indicated that the genetic variance mainly came from individuals within populations, and no genetic differentiation was among populations. Neutral test and mismatch-distribution analysis revealed that the populations of P. esculenta had ever experienced population expansion that occurred in about 0.046 million years ago in the late pleistocene epoch.