Partial sequences of mitochondrial COⅡ gene in 12 octopus species in 2 genus of Octopodinae, were amplified and sequenced to investigate the phylogenesis of Octopodinae in China coastal waters. Multiple biological softwares were employed to analyze the sequence variations and nucleotide composition. Genetic distances were calculated by Kimura-2-parameter method and phylogenetic trees were constructed by both NJ and UPGMA method with more cephalopoda sequences available in GenBank. Results showed that COⅡ genes of octopus were rich in A and T nucleotide bases, as most other mitochondrial genes represent. The sequences showed an obvious anti-G bias. The most variable sites among species lay in the last site of codon of the coding region, leading to less amino acid variation. Genetic distances calculated between species were 0.000 0~0.232 3, and most of them were between 0.140 0 and 0.200 0. The constructed phylogenetic tree suggested that the 12 Octopus species were from two groups: long-arm group represented by Octopus vulgaris and short-arm group represented by O. aegina, which again supported the non-monophyletic of Octopus genus. The Octopus genus can be divided into two or more distant genus according to this study. The taxonomic position of some Octopodinae species was also discussed, and the potential application of COⅡ gene in cephalopoda classification and phyletic evolution was suggested. The results of this study may help understanding the taxonomy and phyletic evolution of Octopodinae species in China coastal waters and contribute to better exploitation and farming of these precious species.