We report the characterization of 15 new single nucleotide polymorphism markers for a threatened species, the chimpanzee (Pan troglodytes), developed using a targeted gene approach. These markers are derived from the Y chromosome and autosomal regions of the genome and show frequency differences between chimpanzee subspecies from central and western Africa. These single nucleotide polymorphism markers are the first to be designed for the genotyping of wild chimpanzee populations and will provide a useful addition to the genetic tools employed for the conservation management of this threatened species.