Seed-consuming rodents are increasingly recognized for their roles in the maintenance of tree species diversity, by acting on crucial post seed-dispersal processes. Yet, studies examining the extent to which rodents may act as secondary seed dispersers and/or predators in Madagascar's forests are limited. Thread-marking seed experiments were run to address this, using the seeds of two native large-seeded, frugivore-dispersed tree species (Abrahamia thouvenotii and Cryptocarya crassifolia), in disturbed and less-disturbed habitats in the rain forests of Ranomafana National Park, during the dry season. Data show that post-dispersal handling of seeds by rodents (predation and removal) was significantly lower in disturbed than in less-disturbed habitats (1.31–3.78 times lower; n = 2200). Also, seeds were more likely to be predated or left on the forest ground after removal than being larder- or scatter-hoarded: 27–78% of the removed seeds were found on the ground, <12% found in burrows and there was no evidence of scatter-hoarding (n = 132). Based on pictures from camera traps, the native rodent species, Nesomys rufus, was potentially responsible for seed predation and/or removal in the less-disturbed habitat; but no indication of the rodent species active in the disturbed habitat was obtained. The lack of scatter-hoarding suggests a limited role of rodents in secondary seed dispersal in this system. These findings form a preliminary account of the potential roles of rodents in post seed-dispersal processes in Madagascar's forests, but this warrants further study.