Abstract: In order to find out the infectious status and the strains differentiation of CSBV in an Apis cerana apiary in spring season in Mengzi, Yunnan Province. The detection of the infection rate and the hereditary variation of CSBV for 57 Apis cerana austro-yunnanensis colonies by RT-PCR. The results showed that: 26 colonies were infected with CSBV in the apiary, and the infection rate was 45.6%. The occult infection rate was 31.57%, and the apparent infection rate was 14.04%. The two pairs of primers could identificate CSBV in Apis cerana austro-yunnanensis, and the second pair was better. RNA sequence variation among the populations was analysed, which displayed that Yunnan population and Chongqing population clustered a branch, and the genetic distance was 0.014. Spring season were important period for occurrence of CSBV in Mengzi, Yunnan Province. It should be taken early precautions. CSBV strains existed variation phenomenon in different regions. The genetic relationship between Yunnan population and Chongqing population was close. It was hypothesized that CSBV geographic distance and genetic distance might have a relationship.