Objective To investigate the type of plasmid map of Y. pestis in the R. opimas natural plague loci in Junggar Basin. Methods A total of 39 plasmid DNA of Y. pestis which were isolated from the natural plague loci of Junggar Basin, Tianshan Mountain, Kunlun Mountain, Qinghai-Tibet Plateau and In-ner Mongolia were extracted by the methods of Kado and Liu. The plasmid map was analyzed by the methods of agarose gel eleetrophoretogram. Results Two types of plasmid map were found in 26 Y. pestis which were isolated from Junggar Basin. Of them 23 were 6 × 106, 45 × 106 and 65 × 106 type of plasmid map, and 3 were 6 × 106, 45 × 106 and 72 × 106 type. Conclusion There are two types of plasmid map in the R. opi-mus natural plague loci in Junggar Basin. One type, which is the dominant type in this area, is 6 × 106, 45 × 106 and 65 × 106 type. This type is also similar to the dominant plasmid map type of the nature plague loci of Tianshan Mountain, Kunlun Mountain, Qinghai-Tibet Plateau and Inner Mongolia. The other type is 6 × 106, 45 × 106 and 72 × 106 type, and this type is new plasmid map type of Y. pestis in our country.