Habitat loss and fragmentation are primary threats to biodiversity worldwide. We studied the impacts of habitat loss and fragmentation on genetic connectivity and diversity among local aggregations of the California gnatcatcher (Polioptila californica californica) across its U.S. range. With a dataset of 268 individuals genotyped at 19 microsatellite loci, we analyzed genetic structure across the range using clustering analyses, exact tests for population differentiation, and a pedigree analysis to examine the spatial distribution of first-order relatives throughout the study area. In addition, we developed a habitat suitability model and related percent suitable habitat to genetic diversity indices within aggregations at two spatial scales. We detected a single genetic cluster across the range, with weak genetic structure among recently geographically isolated aggregations in the northern part of the range. The pedigree analysis detected closely related individuals across disparate aggregations and across large geographic distances in the majority of the sampled range, demonstrating that recent long-distance dispersal has occurred within this species. Genetic diversity was independent of suitable habitat at a local 5-km scale, but increased in a non-linear fashion with habitat availability at a broader, 30-km scale. Diversity declined steeply when suitable habitat within 30-km fell below 10%. Together, our results suggest that California gnatcatchers retain genetic connectivity across the majority of the current distribution of coastal sage scrub fragments, with the exception of some outlying aggregations. Connectivity may help support long-term persistence under current conservation and management strategies. However, emerging structure among more remote aggregations and associations between available habitat and genetic diversity also suggest that continued loss of habitat could threaten diversity and connectivity in the future.