Abstract White spot syndrome virus (WSSV), Taura syndrome virus (TSV) and infectious hypodermal and haematopoietic necrosis virus (IHHNV) have been responsible for major pandemics affecting the shrimp farming industry. Shrimp samples were collected from eight farms in Hainan Province, China, during 2007 and analysed by polymerase chain reaction (PCR) or reverse transcriptase PCR methods to determine the prevalence of these viruses. From the eight sampling locations, only samples from one farm did not show any indication of infection with WSSV, TSV or IHHNV, while samples from one additional farm exhibited evidence of infection with TSV only. Surprisingly, evidence of co-infection with TSV and IHHNV was found among samples at two farms while evidence of co-infection with all three viruses (WSSV, TSV and IHHNV) was detected among shrimp samples at four farms. To further elucidate the molecular characteristics of WSSV in China, we further analysed genomic features of WSSV isolates based on the ORF23/24 variable region. From these data, we identified two novel WSSV strains which contain nucleotide deletions of 5657 and 11093 bp, respectively, when compared with the largest WSSV-TW isolate.