Micromammalian fossil sequences of two classical archaeological sites, Cueva Traful I (CTI) and Cueva Epullán Grande (LL), both in the province of Neuquén, northwestern Patagonia, Argentina, were studied. These sequences cover the entire Holocene, with assemblages mainly composed by rodent and marsupial remains accumulated by owls. Both sites are located near the ecotone fringes of the major vegetation units currently present in Patagonia: Forest-Patagonian steppe (CTI) and Patagonian steppe-Monte desert (LL). Comparisons between fossil and recent owl pellet samples in a regional approach indicated that micromammal communities remained stable over the major part of the last 10 ka, with some minor expansion of desert adapted taxa to the west since the middle Holocene, and a dramatic change in the assemblages during the last 100–150 years. Two alternative but not contradictory explanations can be presented to interpret the stable period. First, climate-environmental changes were not of sufficient magnitude to produce a clear reorganization of micromammal communities. Forest did not invade CTI surroundings, and Monte did not reach around LL. Second, the basic structure of northwestern Patagonian steppe micromammal communities was resilient to minor or moderate climate-environmental changes. The strong shift depicted in the studied sequences in very recent times (100–150 years) can be linked to human impact on the regional environment. This change involves a deep restructuration of small mammal communities ranging from virtual extirpations of some species to dramatic increments of opportunistic taxa. A century of sheep overgrazing, coupled with the introduction of exotic shrubs, was the main factor driving the configuration of present small mammal assemblages in northwestern Patagonia.