A phylogenetic analysis of Rhus (Anacardiaceae) was conducted using nuclear and chloroplast sequences. The nuclear (Nia-i3) and chloroplast (trnC-trnD) sequence data generated in this study were compared with previously published phylogenies of Rhus based on nuclear ribosomal ITS data and chloroplast trnL-F and ndhF sequences. The Nia-i3 data provided more parsimony-informative characters than ITS; the trnC-trnD data provided the most parsimony-informative characters among three chloroplast markers. All data sets support the monophyly of Rhus. Within Rhus, nuclear data support the monophyly of subgen. Lobadium and the monophyly of subgen. Rhus. Chloroplast data suggest a paraphyletic subgenus Lobadium with R. microphylla and R. rubifolia of subgen. Lobadium placed within subgen. Rhus. Rhus coriaria and R. michauxii of subgen. Rhus also have discordant positions in cpDNA and nuclear trees. Each species with discordant positions (R. coriaria, R. microphylla, R. michauxii and R. rubifolia) has a single allele or different alleles of the same species forming a monophyletic group in the nuclear ITS and Nia-i3 data. Incongruence among nuclear and chloroplast datasets, together with the phylogenetic positions, sympatric distributions, and morphological intermediacy of discordant taxa, suggest possible reticulate evolution among members of Rhus.