Non-invasive genetic sampling has been increasingly used to obtain demographic data for rare or elusive species, though its application to small mammals is still tenuous. Here, we explored the utility of non-invasive genetic sampling to provide insights on population dynamics of the near-threatened Cabrera vole, Microtus cabrerae, in a relatively large (250 ha) and highly dynamic Mediterranean farmland area from SW Portugal. During one year, we conducted intensive sampling of fresh scats on four occasions (late Autumn, Winter, Spring, and early Autumn). After identifying genotypes, we used capture-mark-recapture modelling techniques to estimate variations in population size and individual survival, while controlling for heterogeneous recapture probabilities. We found that population variations were in general agreement with previous studies based on life-trapping, peaking from Winter to Spring, and being lower in both Autumn surveys. However, density estimates were notably lower than those reported in less intensive farming systems. Recapture rates were negatively affected by genotyping success, and were higher for males. After controlling for these effects, we found that survival estimates were positively (albeit weakly) affected by population size, and were relatively higher for males. Reasons for such male-biased survival are uncertain, but may be related to possible female-biased dispersal, as predicted by the resource competition model for monogamous species. Overall, our study provides evidence that non-invasive genetic sampling yields useful insights into the ecology and population dynamics of rare and elusive small mammals, such as the Cabrera vole, which may be valuable for guiding management and conservation planning.