Technical Abstract: Single and low copy nuclear genes represent a source of multiple, unlinked and independently-evolving loci, the ideal data set for molecular phylogenetic inference due to their high rate of synonymous substitution compared to chloroplast or mitochondrial genes. The WRKY gene family of transcription factors regulates several diverse, ancient, and highly conserved plant-specific networks including plant defense responses to biotic and abiotic stress; seed, embryo, and trichome development; and regulation of sesquiterpene, starch, and anthocyanin anabolsm. WRKY proteins contain highly conserved domains. The coding region of the highly conserved functional DNA binding domain is commonly interrupted by an intron. Partial sequences of several WRKY loci, originally isolated from Theobroma cacao with a single pair of degenerate primers, were assessed for their phylogenetic utility. Primers designed specifically to amplify individual T. cacao WRKY loci were tested across the sister genera Herrania and Theobroma with Guazuma ulmifolia as the outgroup. The combined WRKY matrices performed as well or better than other genes in resolving the intrageneric phylogeny of Herrania and Theobroma. The ease of isolating numerous, independent WRKY loci with degenerate primers, combined with amplification using primers specific for each locus, renders the WRKY gene family as extremely useful for generating multiple, single- or low-copy nuclear loci for molecular phylogenetic studies at lower taxonomic levels.