Banana streak viruses (BSVs) are double-stranded DNA pararetroviruses causing banana streak disease. Recently, numerous outbreaks of the disease occurred in many banana-producing areas in interspecific hybrids (Musa acuminata × Musa balbisiana) originating from virus-free parents. These infections correlated with the presence of endogenous banana streak viruses (eBSVs), viral DNA sequences integrated in the M. balbisiana genome only. Although integration is not needed for the viral replication cycle, some viral integrants are infectious under stress conditions by reconstituting a replication-competent genome after possible homologous recombination events. Even though the wild M. balbisiana Pisang Klutuk Wulung (PKW) harbours infectious eBSVs, it is resistant to BSVs. We characterised the genetic and genomic endogenous viral organisation of three BSV species in PKW in order to determine the species responsible for the viral expression in the interspecific F1 progeny.