White spot syndrome virus (WSSV) is highly pathogenic to penaeid shrimp and has caused significant economic losses in the aquaculture industry worldwide. With the constant expansion of the areas and scale of prawn farming, variations between different strains of WSSV have emerged. The differences between isolates may cause variations in the virulence of WSS. Deletions in the ORF14/15 and ORF23/24 variable regions have been used as molecular markers to study the epidemiology of the virus. The repeat units of ORF75, ORF94, and ORF125 vary in different isolates and the numbers of repeat units in these three genomic regions are a useful marker for epidemiological studies and for genotyping strains of WSSV. However, each repeat unit may contain single-nucleotide polymorphisms (SNPs) that are important for differentiating haplotypes with the same numbers of repeat units. The results of epidemiological studies may differ if the variability provided by these SNPs is not considered and only the number of repeat units is taken into account.To understand the variations in WSSV ORF14/15 and ORF23/24 and the variable number of tandem repeats (VNTR) and SNPs located in ORF75, ORF94, and ORF125 in different regions of China, we investigated 64 samples that were WSSV-positive on PCR, collected in a disease outbreak area between March and December 2013. The tested samples were from Hainan, Guangdong, Guangxi, Zhejiang, Shandong, Hebei, and Tianjin. Using specific primers, WSSV-positive samples were genotyped with PCR and the amplified fragments were ligated to a T-vector and used to transform Top10 cells. The positive clones were selected and sequenced. After sequencing, the fragments deleted from ORF14/15 and ORF23/24 in different samples were compared with the sequences of Th-96-II and TW respectively, and the three WSSV VNTR regions and SNPs in ORF75, ORF94, and ORF125 from different samples were analyzed with the DNAMAN software. The results showed that there were five samples which had the products of ORF14/15 amplification, and one sample had the products of ORF23/24 amplification. The lengths of the amplified fragments of ORF14/15 were 1267 bp, 1270 bp, and 1892 bp, corresponding to deletions of 6533 bp, 6530 bp, and 5908 bp, respectively, compared with Th-96-II. One type of ORF23/24 was confirmed in this experiment, and the amplified fragment was 1140 bp, corresponding to a deletion of 12070 bp compared with the TW isolate. No fragment was amplified from ORF75. Four different ORF94 VNTRs, including 0, 3, 4, or 12 repeat units, were identified. The ORF125 VNTR, which included 0 or 7 repeat units, was identified. The SNP analysis showed that the bases on the special site in this study were different from the reported types. The bases at site 48 in ORF94 were T, T, T(Type I: 3 RUs), or the bases at site 48 were T, T, T, T(Type II: 4 RUs), and the base were T and 11 A(Type III: 12RUs), respectively. The bases at site 8, 18, 25, 66, and 69 in ORF125(contained 7 RUs), were G, G, G, G, and A, respectively. It is noteworthy that there were also some variations at sites 9, 50, 53, and 61 in ORF125. These results suggest that there are certain degrees of prevalence and variation in WSSV, which causes white spot disease in most parts of China, with clear variations between the different strains in ORF14/15, ORF23/24, ORF75, ORF94, and ORF125.