With the discovery of previously unreported populations of hemoglobin-possessing Ophiactis from the Texas coast in the Gulf of Mexico, an investigation into its population structure, including populations of O. simplex from the Pacific coast of California and O. rubropoda from the Atlantic coast of Florida, was undertaken using DNA sequence data from the mitochondrial COI gene. The reconstructed haplotype network suggests that California populations contain the ancestral source of mtDNA variation, and there is no evidence of recent introductions into Texas. Population genetic analyses reveal the California, Florida, and Texas Ophiactis populations to each be significantly differentiated from one another. Sequence divergence among the three areas is shallower than would be predicted given biogeographic history. Texas and Florida populations are equally genetically diverged from California populations as they are to one another, despite the greater potential for gene flow between these areas. The genetic distinctiveness of the Texas populations and the concordance of this pattern with phylogeographic patterns in other brittle star systems indicate an isolated and independent evolutionary history and we hypothesize that the three geographic regions included in this study each serve as hypotheses of population-level lineages that remain to be tested with independent sources of data.