Inter-specific Musa hybrids have been found to be infected with several Banana streak pararetrovirus strains (BSV-Obino l'Ewai (BSV-Ol), BSV-Imové (BSV-Im) and BSV-Gold Finger (BSV-GF) strains) resulting from activation of BSV endogenous pararetrovirus sequences (EPRVs) integrated into the Musa genome rather than from external sources of infection. The process of genetic hybridisation may be responsible in triggering episomal expression of the BSV integrants. In order to test this hypothesis we carried out a genetic analysis of BSD incidence in a F1 triploid (AAB) population produced by hybridisation between virus- and disease-free M. balbisiana (BB) and M. acuminata (AAAA) parents. Molecular AFLP markers were identified in the M. balbisiana genome only. Analysis of the segregation of these markers allowed the construction of a genetic map containing the locus associated with BSV infection called BSV Express locus (BEL). The BSV-Ol and BSV-Im strains appeared in almost all diseased hybrids while the BSV-GF strain appeared only in about half of these hybrids. Genetic analysis resulting from AFLP results showed that BSV-Ol and BSV-Im EPRVs' expression depends on the same genetic factor, the BEL locus. Although the BSV-GF is not genetically linked to the BEL locus, its appearance and the activation of corresponding EPRV(s) seem to be also subordinated to the BEL locus. So, the discovery of several BSV EPRVs linked to BEL locus implicates that BEL differs in nature from BSV EPRVs.