Edible banana and plantains of the Musa genus are important staple food crops cultivated in humid tropical and subtropical climatic zones. These crops are important for subsistence farming in rural communities and also to generate significant employment and income. In an effort to increase the genetic variability of available cultivars, indexed accessions have been introduced into a regional collection in southeastern Mexico, through the Banana Bioversity International Program. The aim of this study was to use the fluorescently labeled sequence-related amplified polymorphism (SRAP) molecular marker system to characterize the genetic variability within 71 accessions of the existing collection and resolved uncertainties for the better management of the collection, as a preliminary step to establishing a breeding program. These accessions, which included wild species and cultivars of different subgroups, were consistently identified and separated by SRAP markers. A total of 330 polymorphic bands were detected using 12 primer combinations. The average number of polymorphic bands per primer pair was 27.5. The genetic similarity between accessions ranged between 0.44 and 0.97, as estimated using Jaccard's coefficient. Moreover, SRAP