1.Species interact with each other and their environment over a range of temporal scales, yet our understanding of resource partitioning and the mechanisms of species coexistence is largely restricted to modern time-scales of years to decades. Furthermore, the relative magnitudes of inter- versus intraspecific variation in resource use are rarely considered, despite the potential for the latter to influence a species’ ability to cope with changing environmental conditions. 2.Modern desert rodent communities are thought to be strongly structured by competitive interactions, with niche partitioning of food resources hypothesized to explain the coexistence of multiple sympatric granivores. Yet the stability of niche dynamics over extended temporal scales within desert rodent communities is unknown. 3.I examined the isotopic niche dynamics of four common sympatric desert mice (three granivores: Chaetodipus formosus, Perognathus longimembris, and Reithrodontomys megalotis, and one omnivore: Peromyscus maniculatus) in the Smoke Creek Desert of northwestern Nevada using 13C and 15N isotopes obtained from “Modern” (2008-2013 CE), “Historical” (1989-2005 CE), and Holocene fossil specimens spanning the last ca. 7,500 years. 4.I found significant variation in niche position, niche breadth, and interspecific niche overlap of these species through time. The niche breadth dynamics of the cricetids (P. maniculatus and R. megalotis) were positively correlated with one another, while the niche breadth dynamics of the heteromyid C. formosus were negatively correlated with those of all other species. Body size, dietary functional group, paleoenvironmental trends, and time-averaging provided little explanatory power. Importantly, Modern and Historical patterns of resource use and partitioning differed from Holocene baselines in terms of decreased niche overlap and in the absolute and relative position of each species’ niche in at least one isotopic axis. 5.These observations suggest that each species’ resource use changed individualistically over the Holocene, hence niche dynamics are poorly explained by the hypothesis of temporally-stable species interactions at millennial time-scales. Furthermore, changes to the resource base over the last century (likely due to the spread of invasive cheatgrass) may be increasing resource partitioning in the Modern, pushing species past their baseline ranges of resource use variation.