| Summary: | Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by <i>F<sub>IS</sub></i>. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.
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