• Bayesian phylogeny;
  • cryptic diversity;
  • cytochrome b;
  • hybridization;
  • introgression;
  • mitochondrial DNA;
  • phylogeography

For groups of animals with limited or unstable taxonomic resolution, congeneric phylogeographical sampling represents a way to potentially increase resolution of species limits and internal branches during phylogenetic inference. We investigated species limits and whether there was better support for hypothesized relationships among Micropterus (black basses) using wide geographical sampling. Bayesian and maximum likelihood estimates of Micropterus phylogeny including 205 mitochondrial DNA cytochrome b (1140 bp) sequences (150 haplotypes) representing eight extant species and one subspecies recovered eight well-supported clades. Haplotypes from fish identified as Micropterus coosae, Micropterus henshalli, Micropterus punctulatus, Micropterus salmoides, and Micropterus treculii created eight forms of broad-sense polyphyly in the tree, which we hypothesized were the result of incomplete lineage sorting and hybridization-mediated introgression (natural and anthropogenic, i.e. associated with stocking). Our findings mostly agree with hypothesized relationships. However, they provide a more complex view of Micropterus biodiversity, highlighting population-level processes. Our data also provide a useful guide for expanding character sampling (nuclear loci and morphology) to evaluate the history, distinctiveness, and geographical distributions of genetic lineages within and among black basses. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 346–363.