To find markers that distinguish the different Cactaceae species, by using near infrared Raman spectroscopy and scanning electron microscopy, we studied the occurrence, in the stem, of solid deposits in five Cactaceae species (Coryphantha clavata, Ferocactus latispinus, Opuntia ficus-indica, O. robusta, and O. strepthacantha) collected from their natural habitats from a region of México. The deposits in the tissues usually occurred as spheroidal aggregates, druses, or prismatic crystals. From the Raman spectra, the crystals were identified either as calcium oxalate monohydrate (CaC2O4·H2O) or calcium oxalate dihydrate (CaC2O4·2H2O). Opuntia species (subfamily Opuntioideae) showed the presence of CaC2O4·H2O, and the deposition of CaC2O4·2H2O was present in C. clavata and F. latispinus (subfamily Cactoideae, Cacteae tribe). As a punctual technique, Raman spectroscopy seems to be a useful tool to identify crystal composition. In addition to allowing the analysis of crystal morphology, this spectroscopic technique can be used to identify Cactaceae species and their chemotaxonomy.