The genus Musa L. comprises of economically important bananas and has been divided into five sections based on their chromosome number and morphological characteristics viz., Australimusa, Callimusa, Eumusa, Rhodochlamys and Ingentimusa. However, this sectional classification has long been disputed. In this study, we present data on sequenced multiple DNA fragments from the maternally inherited chloroplast genome (atpB-rbcL spacer, trnKmatK intron and psbK-psbI spacer) and the biparentally inherited internal transcribed spacers of nuclear ribosomal DNA of three species of Musa along with data available in GenBank database to understand their implications on the sectional relationship and phylogeny of the genus Musa. In our findings, none of the five sections of Musa previously defined based on morphology was recovered in the molecular phylogeny analysis using cpDNA and nrDNA. Instead, the results corroborate with the suggestion that sectional classification in the genus Musa should be reviewed by combining together the section Eumusa and Rhodochlamys as one and section Australimusa and Callimusa as a single different section, along with that of Ingentimusa.