White spot syndrome has caused significant economic loss in Procambarus clarkii industry in Anhui Province. To understand the molecular epidemiology of white spot syndrome virus (WSSV), we collected nine cultured P. clarkii samples between April and August 2016 from six cities in Anhui Province and performed nested-PCR analyses to detect WSSV and amplify the sequences of ORF94, ORF75 and ORF125 variable regions. The results were as follows: nine samples were all WSSV positive in the first PCR amplification. The numbers of repeats units (RU) in ORF94 were 2, 4, 7, 8 and 12, while 2 RUs was the dominant genotype. The numbers of compound RUs in ORF75 were 3, 6, 9, 10 and 11. The most dominant genotype displayed 9 RUs with the positioning of 45, 102, 45, 102, 3×45, 102 and 45. The RUs numbers of ORF125 ranged from 5 to 9, and the most prevalent genotypes were 7 RUs and 6 RUs.