These data were collected to determine how genetic variation is arrayed across remaining populations of gnatcatchers, allowing inference about individual movement and gene flow patterns among those populations. The work focused on determining the extent to which gnatcatcher aggregations function as an interconnected metapopulation, with aggregations exchanging migrants across a fragmented landscape and freely capable of re-establishing in patches from which they have been previously extirpated. These data will be used in combination with habitat and corridor indices to determine whether genetic connectivity is facilitated by stepping stone arrays of suitable habitat, or whether birds are unable to move across unsuitable habitat regardless of distance. The genetic data will also provide information on distances that individual birds will disperse for breeding. These data were used to support the following publication: