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Summary Approximately one‐half of all flowering plants express genetically based physiological mechanisms that prevent self‐fertilisation. One such mechanism, termed RNase‐based self‐incompatibility, employs ribonucleases as the pistil component. Although it is widespread, it has only been characterised in a handful of distantly related families, partly due to the difficulties presented by life history traits of many plants, which complicate genetic research. Many species in the cactus family are known to express self‐incompatibility but the underlying mechanisms remain unknown.We demonstrate the utility of a candidate‐based RNA‐seq approach, combined with some unusual features of self‐incompatibility‐causing genes, which we use to uncover the genetic basis of the underlying mechanisms. Specifically, we assembled transcriptomes fromSchlumbergera truncata(crab cactus or false Christmas cactus), and interrogated them for tissue‐specific expression of candidate genes, structural characteristics, correlation with expressed phenotype(s), and phylogenetic placement.The results were consistent with operation of the RNase‐based self‐incompatibility mechanism in Cactaceae.The finding yields additional evidence that the ancestor of nearly all eudicots possessed RNase‐based self‐incompatibility, as well as a clear path to better conservation practices for one of the most charismatic plant families.