Musa species, comprising dessert and cooking bananas, contribute the fourth most important food crop in developing countries. They are monocotyledons of the Zingiberales order and the Musaceae family. We have compared genomic sequences in two Musa species with orthologous regions in the rice genome. We produced 1.4 Mb of Musa sequence from 13 BAC clones and annotated and analyzed them along with four previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with both eudicot and Poaceae. Comparison with rice revealed microsyntenic regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The distribution of divergence time among Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons between M. acuminata and M. balbisiana revealed highly conserved genome structure and indicated that these genomes diverged circa 4.6 Mya. The sequencing of the entire genome of a M. acuminata dihaploid is in progress and will enable whole genome comparisons, thus refining the above inferences. It will provide a new foundation for locating genes of agricultural interest and support improvement of banana and plantain varieties.