Abstract: Sipunculus nudus is one of the commercially important inshore demersal species. Understanding the population genetic of this species is a critical component of conservation management and artificial reproduction. However, few studies were reported about the genetic variation between wild and cultured population. The current study employed ninety-one mitochondrial DNA control region sequences to analyze the genetic variation of two cultured (Yingpan and Zhulin in Beihai) and four wild (Daguansha, Qinzhou, Fangchenggang in China and Haiphong in Vietnam) populations of S. nudus. Results showed that sixty and eighty-two polymorphic sites were detected in cultured and wild populations based on the 514 bp sequence, respectively. A negative GC-skew was found in mtDNA control region sequences of S. nudus. Eighty-five haplotypes were identified from control region sequences, among which 4 haplotypes were shared by all populations except Yingpan. According to the Median-joining network, the Hap5 was the chief ancestral haplotype of S. nudus. The average nucleotide diversity (P_i) (0.01514) of cultured populations was slightly lower than the wild populations (0.01531), and all populations had the same haplotype diversity (H_d). The order of genetic diversity for six populations was:YN > YP > QZ > FC > ZL > DG. No significant (P>0.05) genetic differentiations were detected among populations in terms of the genetic distance and fixation index (F_st). The AMOVA analysis indicated that the genetic variance mainly appeared within populations (99.08%). Non-significant genealogical structures were found from NJ and Median-joining network analyses among populations. The genetic diversity of wild population was slightly higher than the cultured populations. The bottom sowing culture was more beneficial to maintain high level genetic diversity of S. nudus. Meanwhile, the genetic differentiations existed among populations were not significant, and the cultured population accumulated genetic variations try to form its own genetic structure.