The Clapper (Rallus crepitans)and King (Rallus elegans) rails are secretive marsh birds with declining populations. These species hybridize, but the extent and direction of introgression are unknown. The logistical difficulties of marsh research coupled with the secretive nature of rails has resulted in limited information on their ecology and life history strategies. Surveys for secretive marsh birds use acoustic monitoring to detect species and for Clapper and King rails there is substantial overlap in vocalizations making identification challenging. We used molecular markers to increase our understanding of the connectivity of Clapper Rail populations along the east coast and their introgression with King Rail. To that end, we obtained Clapper Rail samples from Connecticut (n = 24), Delaware (n = 46), North Carolina (n = 22), South Carolina (n = 22), Georgia (n = 10), and Louisiana (n = 30) and King Rail samples from North Carolina (n = 30) and Louisiana (n = 18). We also obtained known hybrid samples from Louisiana (n = 15). Preliminary genomic analysis using restriction site-associated DNA sequencing (RAD-seq) methods on 80 individuals from Delaware, North Carolina, and Georgia identified two hybrid rails captured in Delaware saltmarshes. Although few King Rail remain in Delaware, this suggests that on-going hybridization is occurring, which might be contributing to the decline of pure King Rail in the state. We failed to differentiate Clapper Rail samples from Delaware and Georgia populations, however, the Georgia samples were collected in the late fall and thus may have been R. c. crepitans individuals that had migrated to Georgia for the winter. In the future, samples from the additional populations collected during the breeding season will be incorporated into the analysis to better understand the connectivity of Clapper Rail populations across their U.S. range and to detect additional signals of introgression.