Ptychobranchus jonesi (Southern Kidneyshell) is one of the most imperiled freshwater mussels in North America. It is endemic to eastern Gulf of Mexico drainages from the Escambia to the Choctawhatchee River basins. Numerous recent surveys considered it restricted to a single population in the West Fork Choctawhatchee River in southeastern Alabama. We conducted comprehensive (9–15 hr per site) mussel searches in three high-quality reaches of the Pea River, a Choctawhatchee River tributary, to assess microhabitat associations for the Southern Kidneyshell. Habitat features were later used to identify subsequent search localities. We found undetected Southern Kidneyshell populations at a total of seven localities in the Choctawhatchee River Basin, AL. Although widely-distributed, the Southern Kidneyshell is extremely rare (n = 13) and comprised <0.3% of all mussels encountered. Prior surveys may have underestimated the distribution of the Southern Kidneyshell because they were broadly focused and thus did not expend the necessary effort to detect this rare mussel. Targeted searches in preferred microhabitats greatly increased Southern Kidneyshell catch rates and were used to detect four of the seven new populations. These results suggest that extensive searches within high-quality habitats are critical to detecting rare mussels in patchy habitats.