The tidewater goby, Eucyclogobius newberryi, is a small gobiid fish with low dispersal ability that inhabits coastal lagoons and estuaries in California. Analysis of mitochondrial DNA sequence data previously identified six phylogeographic groups within E. newberryi, distributed among three biogeographic areas. Here we describe variation in the cephalic canal system of E. newberryi and investigate whether this variation is distributed geographically in a manner consistent with the previously reported molecular and biogeographic hypotheses. The northernmost populations, around Cape Mendocino, have only fully developed canals. Populations between Point Arena and the Monterey peninsula mostly have complete supraorbital canals. Populations from south of the Big Sur coastline to the Los Angeles region (LAR) show high variability in canal structure. The southernmost populations have only distinctly reduced canals. Thus, in general, morphological data match closely the molecular and biogeographic hypothesis, distinguishing at least four of the same phylogroups in the same three biogeographic areas, with similar evolutionary implications. Reduction of diversity in the north is consistent with post-glacial expansion from central California. Abrupt reduction of diversity in the south is consistent with a more ancient stronger barrier to gene flow in the vicinity of Los Angeles and founder-effects or bottlenecks in the southernmost populations. By examining specimens from populations collected between 1879 and 1955 that subsequently were extirpated, we have refined the molecularly derived phylogeographic hypothesis and show that the break at LAR occurs in close proximity to genetic discontinuities in other species studied in detail.