Habitat fragmentation is particularly severe in the Lower Rio Grande Valley (LRGV) of Texas, where greater than 90% of the native wetland habitat has been replaced by agriculture and urban development. The Brownsville Common Yellowthroat (Geothlypis trichas insperata), a rare subspecies of the Common Yellowthroat restricted to this area, is a good model for studying the effects of this extensive fragmentation on avian genetics and ecology. In this study, three hypotheses addressing genetics and habitat fragmentation were tested: (1) the density of Brownsville Yellowthroats is greatest along the Rio Grande rather than away from the river; (2) individuals found on or near the Rio Grande are more closely related than individuals farther away; and (3) a source-sink metapopulation model is best fit to describe the population dynamics of this subspecies. We used 15 microsatellites to examine the genetic diversity of 128 individuals from Cameron and Hidalgo Counties (Texas) sampled during 2008–2009. The densities of yellowthroats at sites near the Rio Grande were not significantly different from densities at sites farther from the river. Genetic analysis indicated that individuals were as related to each other as would be expected in distant relatives and indicated the presence of a single, admixed population. The results suggest that the Brownsville Common Yellowthroat is able to move freely among isolated habitat patches and that wetlands along the Rio Grande do not act as an exclusive corridor for this species.