Objective To investigate genomic variations of two Chinese Yersinia pestis isolates that were isolated from different plague foci obtained from vaccine strain EV76 from the Yunnan province of China.Methods A microarray containing 12 000 probes covering the entire genome of seven Yersinia pestis and two Yersinia pseudotuberculosis strains,was used.PCR assays were performed to confirm microarray results.Results The gene variations detected included the absence of five genes related to the synthesis of betaine in both EV76 and another sequenced attenuated strain,KIM D27.Several genes related to phage-related membrane proteins were found to be absent in the Antiqua biovar Yunnan strain,485,which was isolated from a rodent plague foci.Conclusion These findings provide initial insight into the distinct strains isolated from natural foci,within their genomic context,including Yunnan Y.pestis strains.This information will be used therefore to establish subsequent comparisons of these sequences with published complete genomes of other strains.