Natural fruit finger drop in bananas is one of the major concerns of producers as well as consumers. The aim of this study was to estimate the genetic diversity among 15 diploid bananas with different levels of resistance to finger drop (RFD) using SSR and ISSR (inter-simple sequence repeat) markers, and assess the possibility of association of bands with RFD variables (v1 and v2) via nonparametric methodologies. Molecular genetic analysis revealed that the dendrogram generated by SSR markers used as co-dominant markers better discriminated the genotypes as to genome constitution, genealogy, and RFD. Although nonparametric tests are limited in terms of inferences, they are very useful when data do not follow normal distribution, such as the case in our study. Bananas are parthenocarpic, which hinders obtainment of representative genetic linkage maps and linkage studies due to small number of segregating populations; a pre-requisite for mapping and QTL studies. Therefore, non-conventional methodologies, such as nonparametric tests, become an attractive alternative to overcome this barrier. In our study, the nonparametric tests, Kruskal-Wallis and Spearman correlation, revealed negative and positive associations with RFD for 12 bands (7 from ISSR markers and 5 from SSR markers) with high positive and negative correlations. The results show potential for future sequencing of bands, obtaining sequence-characterized amplified region markers, validation, and subsequent possibility for application in marker-assisted selection in banana genetic breeding programs. This is the first report of the use of nonparametric statistics in attempt to evaluate the association between fruit finger drop and ISSR bands in Musa spp.