Despite the unprecedented rate of global urbanization, a diverse array of taxa are supported in urban areas. However, the long-term persistence of urban wildlife cannot be guaranteed due to the various adverse effects that come with urbanization, such as resource depletion and reduced gene flow. Accordingly, it is imperative to evaluate the health and viability of urban wildlife, particularly of species that are underrepresented in the existing literature, like herpetofauna. Genomic techniques can provide critical insights into urban wildlife health and population viability. Here, we generated a ddRADseq dataset of 162 Dekay’s brown snakes (Storeria dekayi) among 11 locations with different urbanization magnitudes across New Jersey, USA, and examined the population genetic patterns of this common urban reptile. While genetic diversity was not severely reduced within those populations, we uncovered the presence of genetic differentiation and structuring across them, especially for those from the most urbanized areas. Deviations of interpopulation structure from their geographic distributions might reflect either habitat alteration or human intervention in recent history. Landscape genetic analyses revealed the presence of an isolation-by-distance relationship that was only significant within a short spatial distance of 1,500 m. Most urban populations also displayed lower-than-expected historic migration and diversity rates, but some remained genetically connected and diverse. To conclude, our study can serve as a useful guide for population genomic studies on urban herpetofauna. Based on our results, urbanization is likely to impact interpopulation genetic connectivity, but to have limited effects on intrapopulation genetic diversity of small-bodied, terrestrial urban dwellers.