Parallels between species on historically independent islands have been shown to be a powerful means of testing for the action of natural selection on morphology. Mitochondrial DNA evolution is often assumed to be selectively neutral, but this is difficult to test empirically. Here we show that parallels are present between two species of lizards on the geologically distinct but ecologically similar Lesser Antillean islands of Dominica and Basse Terre (Guadeloupe). These parallels are found not only in morphological variation but also in mitochondrial DNA variation and these are correlated with similar ecological gradients. A morphological cline in Anolis oculatus along the Caribbean coast of Dominica is compared to sequence variation in the cytochrome b gene, which shows exceptionally high variability. Patterns of sequence variation and morphology (especially scalation) are congruent, and are significantly correlated with moisture gradients. Anolis marmoratus on the adjacent island of Basse Terre (Guadeloupe) shows parallel patterns of morphological and cytochrome b variation along the Caribbean coast, and these are also significantly correlated with moisture gradients.