The banana family (Musaceae s.str.; Zingiberales), an economically important tropical group of plants, includes three genera, Musa, Ensete and Musella, and possibly 41 species. We performed phylogenetic analyses of a total of 39 accessions covering 28 species in the Musaceae and five outgroup species using nuclear ribosomal ITS and chloroplast trnL‐F sequences. Outgroups were chosen from the closely related families Lowiaceae, Strelitziaceae, and Heliconiaceae. Our results suggest that Musaceae s.str. is monophyletic. Three main internal clades are well‐supported within the family. The genus Musa is comprised of two of these clades, and Musella plus Ensete make‐up the third clade. The sectional classification system of Musa based on chromosome numbers is not supported by DNA sequence evidence. Both inflorescence orientation (erect or pendent) and chromosomal number in Musa, which were characters traditionally thought to be diagnostic in sectional classification, are homoplasious traits in the family. The disjunct distribution of living members of the genus Ensete in tropical Asia and Africa with a fossil species described from the Eocene of Oregon in North America may be an example of the distributional retreat of the Boreal Tropics. The phylogenetic position of the monospecific Musella as sister to the African clade of Ensete suggests that the single species in this lineage is a highly specialized member not warranting generic status. Evidence from the molecular phylogenetic investigations highlights the evolutionary diversification and biogeographic context of this plant group, and suggests additional taxonomic investigations of both Musa and Ensete are in order.