Morphology has been used to establish interspecific limits in echimyid rodents. However, using only morphology can be problematic, especially for polymorphic or morphologically cryptic species. Recently, combined data sources have been used to recognize and delimit species and have proven to be especially useful for taxonomic resolutions. Makalata is a taxonomically problematic genus that needs revision. Currently, two species are recognized: M. didelphoides and M. macrura. A third species, M. obscura, is considered questionable. Molecular studies demonstrate that diversity in the genus has been underestimated. In the present study, we identified 14 subclades representing potential species in the genus Makalata using molecular and cytogenetic data. Analysis of species delimitation corroborated this hypothesis. Four lineages in the Guiana Shield, currently considered to be a single taxonomic entity in the literature (M. didelphoides) based only on morphology, were shown to be potential cryptic species, differentiated only by molecular and karyotype data. We verified that the name M. didelphoides cannot be applied to any clade or museum specimen without a genetic approach and sequencing of the holotype. We present an amended diagnosis for M. macrura through examination of the original description, sequencing, and karyotype of topotypic samples allowed us to associate with the name M. macrura represented by subclade I in this study. Karyotype data proved to be a powerful tool in differentiating the Makalata species according to different combinations of diploid number (2n) and fundamental number, as for other genera of spiny tree‐rats. Our results demonstrate a heterogeneous status for Makalata, highlighting the importance of using multiple tools to determine the taxonomy of this group and reinforcing the importance of molecular and chromosomal data added to the morphological data to obtain a more accurate picture of the taxonomic diversity of this and other small mammal genera.