1. The prevention and management of transmissible diseases hinges upon understanding host dispersal because it influences distribution of wildlife, affects the rate of disease transmission, and alters the spatial distribution of infection. The relationship between host dispersal and chronic wasting disease (CWD) in cervids is of interest because potential interspecies transmission of fatal prion diseases creates serious risks for wildlife, domestic species, and humans.

2. We used molecular techniques to examine dispersal in a population of Illinois white‐tailed deer Odocoileus virginianus. Sampled individuals inhabited areas with confirmed cases of CWD, a transmissible prion disease of cervids, with additional sampling in uninfected locations. We genotyped 1410 deer harvested through CWD surveillance using 10 microsatellites and measured gene flow, determined population structure and quantified gender‐specific differences in dispersal. Additionally we used spatial autocorrelation and parentage assignments to examine individual movements.

3. Female deer demonstrated philopatry as evidenced by higher levels of genetic structure, positive spatial autocorrelation and maternity assignments within one home range.

4. Male deer were less genetically structured and frequently exchanged genes across >100 km.

5. Synthesis and applications. Dispersal contributes to the spread of wildlife diseases. Therefore, knowledge of wildlife movement patterns can enhance the efficacy of disease control programmes. Our findings show that samples collected for disease surveillance are useful for measuring gene flow and inferring dispersal in white‐tailed deer. High genetic admixture indicates males disperse regardless of landscape features. In contrast, distinct clustering of females demonstrates localized dispersal and philopatry. Taken together, results suggest that CWD surveillance and culling of males should be broadly expanded after an outbreak. Furthermore, surveillance of hunter‐harvested deer can be used to identify locales in which CWD occurs, and this information should be used to focus culling efforts on females within genetically defined clusters (‘matriarchal groups’). Removal of matriarchal groups at those locations will reduce horizontal transmission more than widely distributed population reductions.