Dessert and cooking type banana, including plantain, originate from two progenitors: Musa acuminata (AA) and Musa balbisiana (BB). The last one specie genome hosts infectious allelic forms of endogenous Banana streak virus sequences (eBSVs) of viral species Banana streak OL virus (eBSOLV), Banana streak GF virus (eBSGFV) and Banana streak IM virus (eBSImV). Expression of infectious eBSV alleles in AAB and AAAB interspecific banana cultivars is triggered by biotic and abiotic stresses including tissue culture and interspecific crosses, leading to spontaneous infections by the related viruses and has the potential to cause BSV outbreaks. Therefore, infectious eBSVs are currently the main constraint for breeding, exchanging and cultivating banana interspecific hybrids, although the risk of spreading BSVs through such hybrids cultivation has not been assessed yet. The molecular characterization of eBSV alleles in interspecific hybrids harboring the M. balbisiana genome is instrumental for assessing this risk. In this paper, the molecular characterization in several banana and plantain interspecific cultivars and accessions con- served in germplasm collections and/or cultivated in Cuba is reported. The results showed that all analyzed genotypes harbor infectious allele GF7 except Manzano INIVIT, and that several of them displayed modified eBSOLV allelic patterns. The results also showed that FHIA 01, FHIA 18, FHIA 20, FHIA 21 hybrids and cultivar Manzano INIVIT (AAB) do not present eBSImV sequence.