<p>The Atlantic Forest has experienced a significant loss of its original vegetation, with more than 80% of the biome now comprising small and isolated fragments. To understand species distribution, it is crucial to comprehend the impact of fragmentation on species persistence within this biome. Previous phylogeographic inferences have indicated that <i>Trinomys iheringi</i> and <i>T. dimidiatus</i> are structured into two populations each. In this study, we employed a more comprehensive database to re-examine the phylogeography and conduct a detailed analysis of the demographic history and population structure of two <i>Trinomys</i> species. The results indicate that <i>T. dimidiatus</i> is structured into at least three populations clusters: Serra dos Órgãos, South Center of Serra do Mar, and North of Serra do Mar. <i>T. iheringi</i> is highly structured into two populations: São Paulo and Ilha Grande. The demographic analysis indicated that <i>T. dimidiatus</i> from Serra do Mar exhibited an expansionist trend previously the Last Glacial Maximum (LGM). In contrast, <i>T. iheringi</i> experienced an expansion of suitable areas onto the emergent continental shelf during the LGM. Additionally, <i>T. iheringi</i> includes an entirely isolated island population exhibiting no gene flow, and analysis suggests the presence of a new microendemic species. The results presented here indicate that <i>Trinomys</i> species have complex genetic structure patterns that show the importance of Atlantic Forest ecosystem conservation.</p>