The California Channel Islands have been the focus of multiple conservation studies on charismatic vertebrates and plant species, but very few studies have focused on insects. In this study we examined the phylogeography of Coelus pacificus Fall (Coleoptera: Tenebrionidae), a dune-inhabiting darkling beetle, endemic to the islands. Our aim in this study is to decipher the relationships between C. pacificus and the congeneric species Coelus ciliatus Eschscholtz that is distributed on the mainland, to examine the biogeographic relationships of the islands and augment the conservation efforts on the islands with insect data. We sequenced 235 specimens of Coelus for the cytochrome oxidase I mitochondrial gene. We performed phylogenetic analyses to assess the historical relationships of the different species and islands. We also examined the connectedness of the islands by using pairwise φ;st and hierarchical analysis of molecular variance to test alternate hypotheses of geographical structure, Based on the phylogenetic analyses, C. pacificus is a valid, multi-island endemic species. Haplotypes were grouped into two clades: one clade composed of Santa Cruz, Santa Rosa, San Miguel, and San Nicolas; and the other clade composed of Santa Catalina and San Clemente. The highest haplotypic diversity was observed in San Clemente and San Nicolas islands, but all islands had unique haplotypes. Two haplotypes morphologically indistinguishable from C. pacificus formed a sister clade to C. ciliatus, suggesting either an ancient hybridization event or cryptic speciation. The California Channel Islands should be managed on a system wide basis, at least for some of the organisms or habitats and each island's population requires separate management to protect genetic integrity.