Mating patterns are highly context-dependent and the outcome of selection pressures formed by ecological factors, inbreeding levels and access to available partners. In small and inbred populations, matings are limited by high kin encounter rates and access to mates. In this paper, we use background pedigree data to investigate mating patterns and inbreeding avoidance in an isolated and critically endangered Arctic fox (Vulpes lagopus) population. Empirical data showed avoidance of matings within natal family. Based on 35 documented matings, we only recorded two full-sibling matings and these occurred between individuals from different natal families. Matings between second-order relatives, however, occurred to the same extent as between unrelated individuals. To test how this influenced the population development of inbreeding (f), we simulated scenarios of random mating, exclusion of natal family and exclusion of individuals in already existing pair bonds. The observed development of inbreeding did not correspond the expected scenario of random mating (linear regression, r² = 0.354, P = 0.20), but showed a comparable outcome as the simulated development of discriminating natal family (linear regression, r² = 0.980, P < 0.001). We conclude that behavioural, pre-copulatory inbreeding avoidance strategies occur in this population and that exclusion of mating with natal family causes a slower increase in inbreeding levels compared to random mating. This study demonstrates how long-term monitoring, pedigree construction and simulations can generate information valuable for an in-depth understanding of both conservation genetics and behavioural ecology in threatened populations.