Past and current climatic and environmental changes have contributed to configure actual species distributions and abundances. Knowing their evolution over time allows discrimination between natural and anthropogenic causes in current composition of faunal communities. We evaluate the changes in small mammal assemblages from the north-central Patagonian Andean forests since the Late-Holocene to recent times and their relationship with the environmental modifications driven by human activities. A bone sequence from Población Anticura archaeological site (lower Manso river valley, Río Negro province, Argentina) was studied, which encompasses a time span from the early Late-Holocene (3350 ± 100–2270 ±80 years BP) to final Late-Holocene (1420 ± 70–530 ±50 years BP) and Historical times (480 ± 70–280 ±40 years BP). The species composition indicates that forest environment established in the area from at least the Late-Holocene (dominance of Loxodontomys micropus, with subordinate frequencies of Abrothrix olivacea, A. hirta, Geoxus valdivianus, Irenomys tarsalis, and Paynomys macronyx), with patches of (or near to) open environments (presence of Reithrodon auritus and cavids). It is remarkable the presence of cavids, which increased their abundance in the sequence towards Historical times but disappeared nowadays. The low frequencies (<10%) of the rodent Oligoryzomys longicaudatus along the entire sequence is also relevant, since this rodent is the reservoir of the Andes strain of the Hantavirus (ANDV), which causes pulmonary syndrome. This mouse dominates the small mammal assemblages from forests and ecotonal shrublands of northwestern Patagonia (abundances exceed 50% in owl pellets recently collected from the study area). Current configuration of forest and ecotonal assemblages, particularly the high abundance of O. longicaudatus, should be mainly linked to anthropogenic causes, including the introduction of cattle, land clearing, and the advance of introduced plant species such as the sweet briar ( Rosa eglanteria). Particularly, this exotic shrub offers shelter and additional food for O. longicaudatus, turning their shrublands into spaces of high epidemiological risk.