White spot syndrome virus (WSSV) is a viral pathogen that has caused significant economic losses in shrimp farming. Variable-number tandem repeats (VNTRs) (open reading frame [ORF] 94, 125 and 75), a large deletion (ORF 23/24) and a transposase were proposed as molecular markers for genotyping. WSSV-infected shrimp Litopenaeus vannamei were collected in 2 Brazilian regions (Santa Catarina and Bahia) from 2005 to 2008. DNA was extracted and PCR of the variable regions was performed, followed by sequencing. All Santa Catarina samples showed the same number of repeats for the minisatellites analyzed. Bahia samples showed a different pattern for the regions, indicating that there are at least 2 different WSSV genotypes in Brazil. Both Brazilian isolates have an 11453 bp deletion in ORF 23/24 when compared with WSSV-TW (Taiwan), which has the full sequence for this locus. The Brazilian WSSV isolates were compared with WSSV isolates from other countries in the Americas (USA, Panama, Honduras, Mexico and Nicaragua); the repeat number patterns for the 3 VNTR regions analyzed were different between the Brazilian isolates and the other western-hemisphere isolates. This may be due to mutations in WSSV after its introduction into the different countries. Our results also show that WSSV found in Bahia and Santa Catarina very likely originated from different sources of contamination.