Striped skunks (Mephitis mephitis) act as reservoirs of many zoonotic diseases and are highly adept at persisting in urbanized landscapes in high densities. A better understanding of the interaction between skunks and the urban environment can aid in the development of management approaches to disease outbreaks, as well as provide information on wildlife responses to urbanization-induced habitat fragmentation. We studied the genetic structure of a population of striped skunks in an urban environment, assessing the presence of subpopulation structuring, sex-biased philopatry, and natal habitat—biased dispersal. Analysis of microsatellite data failed to detect any significant population clustering or evidence of natal habitat—biased dispersal, but spatial autocorrelation analyses did reveal patterns of limited dispersal (< 2 km) and suggest female-biased philopatry. Our results suggest that urban habitats provide few barriers to gene flow in striped skunks.