This paper employs nonivasive sampling DNA sequencing technique for estimating molecular phylogeny of 5 Chinese peculiar Parnassius Butterflies. Of 433bp mitochondrial cytochrome b DNA sequences, A% + T% was 75.4%, and 40 nucleotide sites were substituted (about 9.24%). The molecular phylogenetic tree constructed by parsimony method suggests that Parnassius acco is closely related to Parnassius baileyi; Parnassius apollo, Parnassius orlears, and Parnassius simo are independent branches respectively. Parnassius simo is divergent earlier. The result is identical with that of morphology.