The Baja California region provides a natural setting for studying the early mechanisms of allopatric speciation in marine systems. Disjunct fish populations from several species that occur in the northern Gulf of California and northern Pacific coast of Baja California, but are absent from its southern shores, were previously shown to be genetically isolated, making them excellent candidates for studying allopatry. In addition, one of these species, the sargo Anisotremus davidsonii, has two pairs of congeneric Panamic trans-isthmian geminate species that allow for internal molecular clock calibration. Phylogeographic and demographic approaches based on mitochondrial (cytochrome b) and nuclear (S7 ribosomal protein) sequences showed that A. davidsonii entered the gulf from the south, and later colonized the Pacific coast, approximately 0.6-0.16 million years ago. Pacific coast colonization may have used a route either around the southern cape of Baja California or across the peninsula through a natural seaway. However, while several seaways have been described from different geological times, none matches the dates of population disjunction, yet much geological work remains to be done in that area. At the present time, there is no evidence for dispersal around the southern tip of the Baja California Peninsula. Signatures of incipient allopatric speciation were observed, such as the reciprocal monophyly of disjunct populations for the mitochondrial marker. However, other characteristics were lacking, such as a strong difference in divergence and coalescence times. Taken together, these results suggest that disjunct populations of A. davidsonii may be consistent with the earliest stages of allopatric speciation.