Even though molecular clocks vary in rate to some extent, they are widely used and very important in a range of evolutionary studies, not least in interpreting cause and colonization in phylogeography. Evolutionists may use island age and emergence to give the earliest possible date for colonization by a species and hence give the lower limit in a molecular clock calibration. The geology of the Lesser Antilles is well studied and Barbados, although composed of some ancient rocks, is thought to have emerged only about 1million years ago (Ma). The cytochrome b mitochondrial gene is the most widely used gene in vertebrate phylogeography, and generally evolves at a rate of 1–2% per million years (Myr) for poikilothermic vertebrates. Divergence measured across almost all of this gene in the endemic anole (Anolis extremus) reveals a mean patristic distance of approximately 8.3% between this clade and its sister, together with distinct divergence and phylogeographical structure within Barbados. The divergence time, estimated by a range of procedures using four calibration points, is not in the least compatible with the proposed geological time of emergence of Barbados. Hence, either the molecular clock rate does not apply to the Barbadian anole population, or the geological dating of the emergence of Barbados is erroneous. The compatibility of geological times and molecular divergence of this complex on Martinique, together with relative rates tests comparing the rates on Barbados and Martinique, do not suggest atypical clock rates. The question of whether Barbados emerged much earlier than is currently thought, or whether the molecular clock assumptions are inappropriate, remains open.