STR analysis of canine-derived biological evidence for the identification of individuals is becoming an important tool for forensic investigations. A protocol for the multiplex PCR amplification and capillary electrophoresis of nine autosomal STRs and two fixed-size markers for sex identification in dogs and wolves is described here. The selection of the loci included in the multiplex complies with the recommendations of the International Society for Forensic Genetics in regard to human DNA analysis. The protocol is optimized for automatic fragment size detection in an ABI platform.