Abstract: The sequences of cytochrome b were sequenced in the study. Homologous sequences were compared among llama, guanaco, vicuna, Bactrian camel, Arabian camel, and sheep. Base compositions and variance among these regions were calculated. Based on cytochrome b sequences the molecular phylogenetic trees were constructed by methods of Neighbor Joining and Maximum Likelihood, the taxonomic status of alpaca in the camelidae was discussed on the molecular level. The results showed that genetic difference between alpaca and vicuna, llama were comparatively more than genetic difference between alpaca and guanaco. The results made it possible that in the traditional taxonomy alpaca was breeding camel after domestic guanaco, and provided molecular basis for the traditional taxonomy.