The recent rediscovery of Jatropha riojae, which was considered as probably extinct, led to a taxonomic re-evaluation of the species due to its problematic circumscription with respect to morphologically similar species of Jatropha section Loureira subsect. Loureira. Based on our study, J. riojae is accepted, taxonomic clarifications are made, including the designation of a lectotype for the name, a complete description of vegetative and reproductive structures is provided, and the species is illustrated and compared to others with which it has been confused. The geographical distribution of J. riojae is clarified as endemic to the municipality of Acatlán, Puebla, Mexico in the south of the Balsas River Basin. To determine the conservation status of the species, the risk assessment method of the Mexican Red List (NOM 059-SEMARNAT-2010) was applied, indicating that J. riojae should be assigned to the “Endangered” category. A re-evaluation of the species under the IUCN criteria indicated that it should be assigned in the “Critically Endangered” (CR) category.