Abstract: The objective of this study was to examine genetic similarity of C. tenuicollis among populations from different regions, and the phylogenetic relationships with other taenia species. The complete sequences of mitochondrial Cytochrome b (Cyt b) gene were used to investigate the intraspecific genetic subdivision of 33 C. tenuicollis isolated from seven different cities in Sichuan and Yunnan Province, NJ tree and MP tree were constructed using the MEGA version 4.0 software and PAUP version 4.0, respectively. The results showed that the complete sequence of Cyt b gene of C. tenuicollis was 1 068 bp, and 22 haplotypes were detected, homology analysis indicated that the homology identity levels of nucleotides of Cyt b gene among haplotypes were high, ranged from 97.3% to 99.9%, but the homology identity levels of nucleotides of isolates in this study and other 5 kinds of taenia spp. cestodes in taeniidae were below 82%. The phylogenetic trees based on Cyt b gene showed that all the haplotypes of seven populations were formed a single cluster that could be divided into three subgroups. There was no direct relationship to geography or host, appeared disordered distribution pattern which there was not obvious geography cluster or host cluster. There were some genetic differences in Cyt b gene within C. tenuicollis, but no significant variation, while interspecies difference was obvious. It was concluded that Cyt b gene can be used as genetic marker for population genetic studies of cestodes. The results of the present study provided foundation for further studies of population genetics of C. tenuicollis, and for the differential diagnosis of taeniid tapeworm infections.