We investigated the endemic situation of alveolar echinococcosis (AE) in Nileke County,Yili Prefecture,Xinjiang and its genetic diversity of Echinococcus multilocularis.Human AE cases in the county were retrospectively investigated including their location and surrounding ecological conditions.Sequence detection and analysis of nad2,cob gene fragments of AE mtDNA from patients was used to identify genotype variation.Results showed that a total of 48 AE cases were diagnosed and the first AE patient was identified in 1989 in the county.The 45.8％ of AE cases were found in the recent 5 years (2011-2015) and annual prevalence was 1.7 per 100 000.The patients were distributed along the Kashgar River,particularly intensive in Wulasitai Township.The 38.6％ of the patients were aged arranged 35-44 years old,64.6％ were male and 95.8％ were farmers and herdsmen.AE cases were confirmed further and there was only one haplotype by sequencing analysis from 11 AE clinical patients in the county.It suggests that Nileke County is AE foci,and alveolar echinococcosis with sequences conserved is an emerging disease in the county.