White spot syndrome virus (WSSV) is a viral pathogen that continues to cause significant economic losses in shrimp farming. VNTRs are located along the WSSV genome and are powerful tools in the study of the epidemiology and evolution of WSSV and its spread around the world in the last decades. Results of the current study suggest that genotype analysis using the ORF75, ORF94, and ORF125 (van Hulten et al., 2001) loci allows different applications in field epidemiology studies: (1) ORF 75 would be the best marker for the identification of ancestor WSSV isolates in small scale farming areas (shrimp ponds; provinces); (2) tandem repeat sequences in ORF94, followed by ORF125 could be used to discriminate WSSV isolates in small scale systems; (3) genotyping of ORF125 could be especially useful yin investigating mixed genotype WSSV infectins and tracing the relationsjrip between carriers and infected shrimps in pond settings.