Natural variation describes the normal fluctuations that occur in ecosystems over time in the absence of significant human-driven disturbance, providing a buffer that facilitates ecological resilience. Long-term data on ecosystems are useful in developing baselines of natural variation and identifying the limits to resilience within different ecosystems. Here, we examined two contemporaneous vertebrate fossil assemblages of the Naracoorte Caves in southern Australia to determine the magnitude and extent of natural variation and resilience exhibited by a small-mammal paleocommunity through the last glacial cycle (c. 50-10 kyr BP). We also investigated the effect of sampling the assemblages at different timescales on observed patterns of variability and quantified sampling effects to test the robustness of the temporal trends. Our results show that the paleocommunity was structurally and compositionally stable through the early glacial period and last glacial maximum (LGM), with variability exhibited only in species abundances. Significant variability in species abundances, abundance ranks, and species richness during the post-LGM deglaciation reveals paleocommunity reorganization and a loss of resilience to climatic change at this time. A nearby marine-core record suggests that the paleocommunity reorganization was associated with sea-surface temperatures warming past 168C, postdating the onset of warming following the LGM by c. 1-3 kyr. This suggests that the paleocommunity was sensitive to specific temperature thresholds rather than shifts between warming or cooling trends per se. Our results also show that patterns of natural variability are sensitive to time-averaging, which can smooth out rapid and short-term changes and limit our capacity to temporally correlate faunal changes to their environmental or climatic drivers. The responses of the small-mammal paleocommunity conform to models derived from other paleontological and modern assemblages in which changes in species abundances may not always lead to community restructuring.