Long-term persistence of the large mammal lowland tapir is at risk in the largest Atlantic forest corridor

•Two genetic populations (inland and coastal) were found, reflecting the two major forested blocks.•Population genetic structure was better explained by elevation.•Low effective population size was found in both genetic populations.•The largest rainforest continuum is not totally permeable to gene flow of large mammals.•Lowland tapir conservation efforts should be taken even for populations living in large continuous areas.