Map based cloning (MBC) is a forward genetics approach which aims to identify the nucleotide sequences that underlies a specific trait which may be the product of either induced or naturally occurring variation. Quantitative Trait Loci (QTL), the basis of many important agronomic traits, are defined by position and, unless a corresponding mutant can be identified, MBC or association mapping are the only ways to obtain the sequence of genes underlying a quantitative trait. Quantitative trait loci (QTL) are controlled by many loci and environmental factors and therefore the phenotype does not provide reliable genotypic information. However, QTL cloning by MBC has been successful in model plants. The most common problem in MBC is inconsistencies in mapping data. The small population size of segregating offspring from Musa interspecific, interploidy crosses has been regarded as the major obstacle to genetic analysis. However, some progress has been achieved in developing genetic markers and quantitative trait variation in Musa. Genomic resources available for map-based cloning in Musa include, resistance genes, resistance gene analogs (RGA), and RGA genetic markers. Bacterial artificial chromosome (BAC) resources are being used for physical mapping of RGAs in Musa. When compared to other crops of equal or lesser economic importance, platforms (viz.: high resolution genetic maps, mapping populations, ESTs and the whole genome sequence) for map based cloning in banana and plantain, are lagging in development. However, a relatively high density reference genetic map of M. acuminata was recently made public. As this genetic map includes many SSR markers, it should be useful for researchers who do not have access to expensive high throughput technology such as microarray technology.