FT-Raman spectra have been obtained from the highly pigmented lichen Cryptothecia rubrocincta from a Brazilian vestigial rainforest habitat. Spectral signatures of the two main lichen substances, chiodectonic acid and confluentic acid, were identified in adjacent zones of the thallus. Of the characteristic zonal colours displayed by the thallus, the outer red zone contained chiodectonic acid and no calcium oxalate, and graded into by a pink zone with calcium oxalate monohydrate (whewellite) in association with chiodectonic acid, to the inside of which is a concentric white zone containing calcium oxalate dihydrate (weddellite); however, chemically differentiated sites (elliptical brown flecks with a major axis of c. 15 μm) in both the pink and red zones contained chiodectonic acid and calcium oxalate monohydrate. The role of Raman spectroscopy in the spatial identification of lichen substances in the thallial structures is demonstrated.