Tropical crops are seldom, if ever, included in international genome analysis initiatives, but these crops are of paramount importance to the world for socio-economical and ecological reasons. Musaceae are among the tallest monocotyledons and belong to the major basic food-producing plants on earth. Dessert banans are intensively cultivated for export to Europa and North America, while cooking bananas and some dessert bananas are cultivated most often in backyard gardens for local consumption in tropical countries. Although mapping the banana genome is complex due to sub-species specific translocations, comparative map analysis uncovers interesting data on genome structure (i.e. identification of translocation breakpoint) as well on the molecular markers used. Performance of RAPD, RFLP, microsatellite and isoenzyme markers are compared. Depending of the population mapped, the same RAPD markers associate in different linkage groups whereas RFLP markers conserve colinearity. Thus exclusive use RAPD markers for QTL mapping in bananas is risky and QTL analysis should be based on co-dominant markers (i.e. RFLP, microsatellites). Microsatellites may be the "anchor marker" of choice for a banana core map. The present map is based on 82 individuals from F2 type progeny "SFB5". In addition, a self-fertilised progeny, 89 individuals, from a highly fertile synthetic AA diploid (M53), displaying a BLSD resistant phenotype, is being mapped. In particular, the efficiency of polymorphic microsatellite markers for mapping the banana genome with rapid and simple methods is pointed out