The Neotropical freshwater ichthyofauna comprises approximately 16% of the worldwide fish biodiversity, encompassing about 5,200 presently recognized species in 17 orders [1,2]. How- ever, this number is underestimated, as a steadily growing number of studies points on previ- ously overlooked cases of cryptic species and species complexes (e.g., [3–7]). In this context, the contribution of the cytogenetic studies to the knowledge of biodiversity and evolution of the Neotropical fishes is remarkable, providing useful taxonomic and evolutionary data (reviewed in [8]). Additionally, methodological advances in molecular cytogenetics, namely diverse variants of fluorescence in situ hybridization (FISH), allow to decipher karyotype/ genome evolution among related species, including the degree of preserved conserved synteny and the characterization of structural and functional organization of genomes [9–20]. These approaches already helped to document cryptic species diversification [21–29] as well as to track remarkable karyotype stability [30,31], the response of the genome dynamics to environ- mental cues [32] or its correlation with geographic distribution [33].