Based on knowledge of complete mtDNA genome sequences of species already in the NCBI data base, we have developed a PCR-based primer design & sequencing algorithm that will permit amplification of the complete mitochondrial DNA genomes of related species as a series of ordered, contiguous fragments, whose complete sequence can be efficiently determined. Routine collection of genome-sized data sets from multiple individuals per species, together with phylogeographic analysis of completely-resolved intraspecific gene trees, will provide the detailed historical information and necessary statistical power to evaluate vicariance and dispersal phenomena at scales of interest to fisheries managers and population biologists.