Abstract Non‐native species can spread rapidly through aquatic ecosystems in association with both natural and anthropogenic mechanisms, but the relative importance of these two mechanisms in determining the spread of a species is not always clear. The red swamp crayfish (Procambarus clarkii) has been introduced to multiple continents, including waterbodies in the United States where both natural and anthropogenic dispersal are likely to have contributed to its current distribution. The present study combined comparisons of historical and contemporary distributions of P. clarkii and several high conservation priority crayfish species, regional field sampling, and microsatellite‐based genetic approaches from the Pee Dee River basin in North Carolina and South Carolina to understand the dispersal patterns of P. clarkii and its potential effects on native crayfishes. Field sampling and microsatellite analyses revealed widespread populations of P. clarkii throughout the study area with catchment‐specific patterns of population genetic structure, wherein more distinct genetic structures were found in the basin with historic aquaculture activities and a longer period of occurrence. The rapid spread of P. clarkii has occurred concurrently with extirpations of populations of native crayfishes, namely the Waccamaw crayfish (Procambarus braswelli), the Carolina Sandhills crayfish (Procambarus pearsei) and the coastal plain crayfish (Procambarus ancylus). The rapid spread of P. clarkii and coincident extirpation of native crayfishes calls for more extensive regulatory controls to help prevent the intentional or accidental release of non‐native crayfishes through aquaculture practices, bait releases, the pet trade and the environmental education industry.