Chromosome pairing studies at meiosis have revealed that translocations are frequent in banana genomes. In Musa acuminata, seven groups of translocation have been identified (Standard, North Malaysia, Malaysia Mountains, North A, North B, Indonesia, and East Africa). Each group comprises accessions having the same chromosome structure. Translocations increase the difficulty of constructing a genetic map, studying the inheritance of agronomical characters and breeding in general. The objectives of our study were to develop a tool to characterize translocations on chromosomes based on fluorescent in situ hybridization of BAC clones (BAC-FISH) and to use this tool to characterize the translocations in the accessions 'Calcutta 4' (2n=2x=22, translocation group North A) and 'Madang' (2n=2x=22, translocation group Standard). To achieve this, a genetic map and a 'Calcutta 4' BAC library were built, the BAC-FISH technology was adapted to bananas and a banana cytogenetic map was initiated. The genetic map was based on a F2 population from a 'Calcutta 4' x 'Madang' cross. It encompasses 120 markers (20 RFLPs, 81 AFLPs and 19 SSR markers) distributed over 14 linkage groups and covering 597 cM. The 'Calcutta 4' BAC library comprises 55 152 clones with an average insert size of 100 Kb. About 1.5% of these clones present chloroplast and mitochondrial DNA inserts. This library covers 9 to 10 times the banana genome. Linkage group Il (LGII) was chosen to search for translocations since some of its characteristic (such as a high number of distorted markers) suggested that this group contained chromosomes with translocations. Four BAC clones corresponding to 3 RFLPs and 1 SSR loci distributed on LG II were localized on the 'Calcutta 4' and 'Madang' chromosomes. The results showed that the markers involved in the LG II were localized on three chromosomes, whose structure was different in 'Calcutta 4' and 'Madang', with two linked translocations observed in 'Calcutta 4'. In 'Madang', t