ABSTRACT The Quaternary glaciations had great impacts on the historical biogeography of small mammal species. Recent studies have showed the effects of these climatic cycles on the diversification of several Neotropical rodents, but these have focused on species whose distributions do not encompass the tropical Andes. Thus, the influences of these climatic dynamics on the evolutionary history of tropical Andean rodent species remain unknown. The effects of these climatic changes were addressed on Aepeomys lugens and A. reigi, two Thomasomyine endemics from the Cordillera de Mérida in the Venezuelan Andes. The past potential geographic distribution of both species was inferred using an ecological niche modeling approach. The estimations obtained indicated that the availability of the suitable climatic conditions for these taxa has varied in size and location during the last 140,000 years. The spatial projection of the niche models onto the climatic scenarios explored indicates that the effects over the historical distributions were smaller in A. lugens than in A. reigi. These results show that the current geographic distribution of both Andean rodents conceals complex biogeographic histories, and characterizations of the demographic history and genetic diversity will be required to understand the evolution of the genus Aepeomys in the Andes.