Animals use mating traits to compete for, attract, and choose mates. Because mating traits influence mate choice, the divergence of mating traits between populations can result in reproductive isolation. This can occur without associated morphological divergence, producing reproductively isolated ‘cryptic species’ that are visually indistinguishable. Thus, identifying the mating traits in morphologically conservative groups is key to resolving diversity and speciation processes. Lizards contain many such groups, with phylogeographic studies often revealing highly divergent but morphologically cryptic lineages within species. Considering that cryptic lizard species can be sympatric but morphologically indistinguishable, we hypothesize that candidate species will exhibit divergent pheromones and that pheromones will have typically diverged more than morphology. To test this, we used gas chromatography to characterize pheromones (epidermal pore secretions) from 10 genetically divergent lineages of the Bynoe’s gecko (Heteronotia binoei) species complex in northern Australia. Multivariate analyses of pheromone blends and morphology indicate that pheromones are lineage-specific and have diverged relatively more than morphology. Such specificity suggests that pheromones influence behavioral isolation in this morphologically conservative lizard radiation. These results suggest that pheromone data may unlock the tremendous ‘cryptic’ diversity currently being uncovered in many lizard groups.