White spot syndrome virus (WSSV) is currently the most serious viral pathogen of shrimp worldwide with estimated losses in production amounting to hundreds of millions of US dollars per year. Research results to date have indicated extremely high DNA sequence homology for WSSV isolated from widely separated geographical regions, suggesting that a single virus species of unknown origin has rapidly spread throughout the world since the first report of serious shrimp mortality caused by WSSV in China in 1993. By contrast, we have found surprisingly high variation in the number of 54 bp DNA repeats in the WSSV ribonuclease reductase gene from 55 shrimp ponds (65 samples) of WSSV infected shrimp from Thailand in 2000 and 2002. These were discovered by polymerase chain reaction (PCR) amplification using DNA template extracted from WSSV infected, cultivated shrimp and using primers (Wrb6r-F 5' TCT ACT CGA GGA GGT GAC GAC3' and Wrb6r-R 5' AGC AGG TGT GTA CAC ATT TCA TG 3') located upstream and downstream of the repeat region. These were derived from data for 3 complete WSSV genome for the samples examined. The majority (about 32%) had 8 tandem repeats but others had as few as 5 (about 14%, indicating substantial strain variation in terms of tandem repeat groups. Extracts prepared from individual shrimp in the same outbreak pond belongd to the same repeat group while those collected at the same time from separate WSSV outbreak ponds or from the same ponds at different times tended to belong to different repeat groups. This suggested that the outbreaks were caused by different WSSV isolates. The number of repeats and the sequence within the repeated region showed highly stable. The ORF 94 repeat region has potential for use in epidemiological work with WSSV and may help in tracing its origin and spread.