Genetic variability and structure in Octopus minor was investigated from 154 individuals using mtDNA ATPase 6, sampled from Dalian, Dongshan, Nantong, Qingdao, Shanghai, Wenzhou, Xiamen, and Zhoushan China. Based on 672 bp fragment of Mitochondrial DNA subunit ATPase 6, thirty haplotypes and 140 polymorphic sites were noted, whereas (0.740, 0.048) high and low haplotype and nucleotide diversity observed. The data was further tested with AMOVA that validates 91.24% variation among populations and 8.76% within population. Genetic fixation index was also calculated as 0.91243*. The neighbor-joining phylogenetic analysis revealed three lineages. The Dongshan population distinctly has shown separate lineage. The haplotype networking has shown that Hap1 contributed 48.051% and appeared in six populations whereas, Hap6, Hap11, Hap 16 and Hap17 were also shared by some populations, rest of the haplotypes were unique. This study solely provide species specific information on its genetic structure and population variability in Chinese waters.