【Aim】 To reconstruct the phylogeny of the known species of Anopheles subgenus Cellia from China based on mtDNA-COⅡ and rDNA-28S-D3 sequences, and to interpret the interspecific genetic relationship among them. 【Methods】 mtDNA-COⅡ and rDNA-28S-D3 genes of 20 species in subgenus Cellia and 2 species in subgenus Anopheles of genus Anopheles were sequenced and analyzed. The trees of neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) of these species were constructed based on COⅡ, D3 and COⅡ with D3 conjunction dataset, with Anopheles (An.) sinensis and An. (An.) hyrcanus as the outgroup. 【Results】 The length range was 685 bp for mtDNA-COⅡ and 375-410 bp for rDNA-28S-D3, and the level of pairwise genetic distances among Cellia mosquitoes was 0.015-0.117 for COⅡ and 0.003-0.111 for D3 gene. All the phylogeny trees showed that the outgroup was divergent. The Neomyzomyia series was monophyletic, but paraphyletic in COⅡ tree. The relationship between Myzomyia and Neomyzomyia was close. The 50% consensus tree by COⅡ with D3 conjunction dataset showed that the 20 species in subgenus Cellia from China were clustered to 4 major clades, and all members of each series and group were respectively clustered together with above 50% bootstrap value, except Anopheles (Cellia) pseudowillmori not clustered within the maculatus group. 【Conclusion】 This molecular phylogeny clearly showed the interspecies and interseries genetic relationship among Chinese subgenus Cellia mosquitoes, and could be useful for the taxonomy and control measures.