I examined the geographic distribution of genetic variation in the livebearing freshwater fish Brachyrhaphis rhabdophora in northwestern Costa Rica as revealed by allozymes and mitochondrial DNA sequences. Allelic variability at 11 enzyme‐coding loci surveyed across 12
localities revealed marked genetic differentiation among populations within drainages (0P= 0.36) and among drainages within regions (0D=0.17), but not between northern and southern geographic regions (0R=– 0.02). Allozyme variation was hierarchically
organized such that populations found within stream drainages were more similar to each other than to populations found in adjacent drainages, a result confirmed by cluster analysis. In contrast to the allozyme data, there was extremely little DNA sequence variation among populations in the
mitochondrial control region (3 variable nucleotide positions out of 444 bp examined). The difference in genetic divergence between allozyme and mtDNA markers was unexpected and is discussed in terms of biogeographical colonization events and a molecular selective swéep on the mitochondrial
genome, both processes that could explain the lack of mitochondrial variability in this highly subdivided species.