Premise of the study: Single-nucleotide polymorphism (SNP) primers were developed for a native North American desert fig, Ficus petiolaris (Moraceae), to provide markers for population genetic studies designed to quantify patterns of gene flow across a complex landscape. Methods and Results: Transcriptome sequencing and bioinformatic protocols were implemented to discover SNPs in single-copy protein-coding genes. Multiplexes of 30 nuclear and 24 organellar (chloroplast and mitochondrial) SNPs were selected for primer development and genotyping on the Sequenom MASSArray System. Of these 54 loci, 49 reliably amplified across a panel of 96 F. petiolaris individuals. Conclusions: This study has provided SNP primers that can be applied in future studies investigating population genetics of F. petiolaris and its coevolution with associated pollinating and nonpollinating fig wasps.