Cultivated bananas are derived from hybridization events between Musa species and subspecies that differentiated in the South East Asia-New Guinea region. These hybridizations generated diploid and triploid inter(sub)specific hybrids with impaired fertility. Some of them, having seedless parthenocarpic fruits, were selected by humans and further dispersed through vegetative propagation. The genomes of these cultivated bananas are expected to have gone through few rounds of recombination and to be organized in a mosaic of large blocks of sequences from different ancestral origins. To characterize mosaic genome structures of bananas, we identified a set of SNPs from WGS data. We applied a hybrid strategy comprising multivariate and SNP clustering approaches as well as a private alleles approach to identify 11 genetic pools that contributed to cultivars and to define specific alleles for each of these genetic pools. The presence of these ancestry informative alleles as well as their ratio were analyzed along chromosomes in order to determine the contribution of genetic groups along chromosomes of cultivated banana. The methodology described here allowed to identify specific alleles for each genetic pool with very few representatives that were sometimes introgressed. With this approach, we also identified informative alleles for two ancestral contributors for which no pure representatives were available and we determined their contributions to cultivars. Based on the identified ancestry informative alleles, we also developed a method to analyze recombination breakpoints between distinct genetic pools in cultivated accessions. This allowed to propose a hypothesis on their origin.