Comparative phylogeographic analyses provide a means to examine the influence of past abiotic changes on species distributions, as drastic or rapid landscape changes are expected to produce congruent phylogeographic patterns across multiple taxa. Despite the unparalleled biodiversity of the Neotropical Region, phylogeographic studies in this domain remain limited, particularly concerning the aquatic biota of Atlantic Forest rivers. The species Mimagoniates microlepis and M. sylvicola were selected as models for this study because they are co-distributed in the Northeastern Mata Atlântica Ecoregion (NMAF). The aim of this study was to investigate, describe, and analyze the phylogeographic pattern of these species in the NMAF. For this purpose, we analyzed mitochondrial DNA from samples collected across the known distribution of the species within the area of interest. Haplotype networks were constructed and comparatively analyzed based on a distribution map of the species, which was also created in this study. The results indicate that, for M. microlepis, five distinct haplotypes were identified, distributed across five different drainages, with only one shared between different localities. For M. sylvicola, 12 distinct haplotypes were identified across seven drainages. The absence of shared haplotypes suggests significant phylogeographic structuring in M. sylvicola, further supported by the high number of mutational steps separating the haplotypes. Interestingly, this study found intraspecific structuring in M. sylvicola but no significant structuring in M. microlepis. According to the fundamental principles of comparative phylogeography, congruent genetic structuring among co-distributed species typically occurs due to a shared biogeographic history. However, although such a pattern was expected within the same genus, the results of this study reveal that the Mimagoniates species in the NMAF display incongruent genetic distribution patterns. This discrepancy may reflect distinct biogeographical or evolutionary histories that require further investigation.