There are presently four recognized species of clinid (kelpfish family: Clinidae) on the west coast of North America: Gibbonsia elegans, G. metzi, G. montereyensis, and Heterostichus rostratus. In addition, Clark L. Hubbs proposed an endemic subspecies in the genus Gibbonsia on Guadalupe Island. Later investigations using allozymes indicated low levels of genetic diversity between populations and treated subspecies names as synonyms, leading to the present-day status of three species in the genus. Here, we use high-throughput sequencing and a combination of nuclear and mitochondrial markers to revisit the systematics and population structure of the genus Gibbonsia. We find that Guadalupe Island specimens that are morphologically identified as G. elegans form a distinct genetic lineage for both nuclear and mitochondrial markers, supporting Hubbs's hypothesis of a Guadalupe Island endemic, Gibbonsia erroli. Further, we find that while dispersal potential is high for all species in the genus, genome-wide markers and outlier analyses show population structure at short geographic distances, suggesting fine scale environmental variation leading to local adaptation.