The heavily impacted coastal dunes of California are home to numerous invertebrates, but very few studies have examined their phylogeographic patterns. Here, we examine the phylogeography of the flightless fossorial darkling beetle Coelus ciliatus Eschscholtz and the extent to which previously identified phylogeographic barriers for terrestrial and marine taxa can explain its haplotype distribution. We compared 16 localities and 128 specimens along the coast of California by using 826 bp of the COI mitochondrial gene. We used Bayesian and parsimony-based phylogenetic analyses and haplotype network analyses to study the phylogeographic structure of the populations, as well as analysis of molecular variance (AMOVA), isolation by distance and FLUCTUATE to examine the population structure. Our analyses identified 42 haplotypes and significant geographic and genetic structure among populations. Gene flow was limited between populations, and phylogenetic, nested clade, and AMOVA analyses indicate a deep break of the populations into two clades, north and south of Big Sur, near Monterey Bay. Populations between Pt. Conception and Big Sur follow a serial founder event pattern, as indicated by isolation by distance analysis. We did not identify a phylogeographic break at Pt. Conception or the Los Angeles area, but we recovered a deep phylogeographic break at Big Sur that contrasts with a break at Monterey Bay identified in other coastal terrestrial animals.