Rhus pachyrrhachis and Rhus virens are medicinal plant species with important uses in northeastern Mexico. They belong to a complex of Rhus species called “lantriscos”, which are used for medicinal applications. The medicinal effects of these species are based on traditional use, however, they require phytochemical research to validate their medicinal properties, as well as structural characterization for their correct identification during the collecting practice and uses. The phytochemical potential of aqueous extracts from R. pachyrrhachis and R. virens was analyzed by the quantification of total phenolic content (TPC), free radical-scavenging potential, and total flavonoids, with a comparison of four drying methods, and some phenolic compounds were identified. Furthermore, the stems and leaves of both species were anatomically characterized to establish a differentiation. R. pachyrrhachis and R. virens showed similar values of phytochemical contents, although the TPC content (0.17 mg of gallic acid equivalent per gram of dry weight, GAE/g DW) was higher in R. virens. The drying method used affected the metabolite contents, and this behavior was related to the species. Regarding the phenolic compounds, shikimic acid, galloylquinic acid, and gallic acid were identified in both species, however, quinic acid was only found in Rhus pachyrrhachis, while vanillic acid O-hexoside was identified only in Rhus virens. At the anatomical level, the pubescence associated with trichomes on the leaves of Rhus pachyrrhachis was highlighted as the main differential characteristic.