Abstract: Objective To analyze the co-divergence of hantaviruses(HV) with mitochondrial D-loop and cytochrome b(Cyt-b) gene of its rodent hosts in Zhejiang province.Methods The sequences of mitochondrial D-loop and Cyt-b were adopted in the analysis.Total DNA was extracted from HV positive and negative lung tissue samples from Apodemus agrarius.The sequences of the D-loop and Cyt-b were amplified with PCR.The sequence similarity was assessed with Clustal X and the phylogenetic tree was estimated with MEGA using the maximum likelihood method.Results According to the phylogenetic tree,the study indicated that the HV positive and negative Apodemus agrarius were in same cluster.Conclusion There is no obvious relationship between the sequences of mitochondria of the hosts and the infection of hantavirus.