Maned Three-Toed Sloths (Xenarthra: Bradypodidae) are endemic to the highly fragmented Atlantic Forest of Brazil. Both species, known as Northern Maned Sloths (Bradypus torquatus Illiger, 1811) and Southern Maned Sloths (Bradypus crinitus Gray, 1850), exhibit disconnected populations across the distributions. Our study investigates the evolutionary and demographic trajectories of these two sloth lineages, utilizing whole-genome resequencing data compared against a high-quality genome assembly. Our analysis reveals that the Southern Maned Sloth exhibits lower genetic diversity and a smaller historical population size compared to the Northern Maned Sloth. These disparities likely stem from differing environmental and climatic historical changes along the Atlantic Forest distribution during the Pleistocene, which was characterized by greater climate stability and larger refugia areas in the north. Nonetheless, the northern population has experienced a fast increase in inbreeding levels in the last 20 years, in a region of Bahia State with extensive recent deforestation associated with livestock farming, agriculture, and urban development. In addition, the northern lineage presented a higher genetic load, which could imply higher fitness costs for this population if inbreeding patterns persist. Taken together, these results confirm the independent evolutionary paths of these two lineages and underscore the conservation challenges faced due to historical evolutionary events and current deforestation of the Atlantic Forest.