We show the power of detailed AFLP study to address questions of species delimitation and genetic diversity in morphologically-cryptic plants. We have combined this technique with karyological studies to explore species boundaries in the Western Mediterranean representatives of Veronica subgen. Pentasepalae. Several members of this subgenus are represented in the Iberian Peninsula and North Africa by morphologically similar populations, which lead to different taxonomic hypotheses. We have analyzed genetic variation with two different objectives: first, to provide a basis on which one taxonomic hypothesis is favored against its alternatives, and second, to obtain a satisfactory interpretation of phylogeographic patterns. The usefulness of several parameters and analyses is considered in order to help rank taxa and to reveal details of their speciation modes. Some of these parameters are presented with a geographical background to facilitate phylogeographic interpretations. The data support one of the previously proposed taxonomic hypotheses, which results in the recognition of eight taxa. An east-to-west migration route within the Iberian Peninsula is hypothesized, coinciding with the general pattern proposed for Veronica subgen. Pentasepalae. Further data on genetic variability and chromosome counts for 41 populations are provided.