Fourteen populations of Musa acuminata ranging from populations in the lowlands of northern (ssp. siamea) to central Malaysian region (ssp. malaccensis) and highland banana (ssp. truncata) were characterized based on chromosome number and 46 morphological characters. A large amount of variation was observed within the populations. However, only highland bananas appeared morphologically distinct. Lowland populations both from northern and central Malaysia were found to be overlapping and no distinguishing pattern was observed. The morphological characters found variable within these populations were related to developmental changes and mutations. The results obtained in this study were not revolutionary. However, the survey of a large number of characters treated with multivariate techniques further sharpened the existing groupings of the Musa acuminata subspecies.