Although synanthropic invasive murid rodents are freely traded in pet shops in South Africa, their taxonomic identities, however, remain largely unknown. Twenty-four murid rodents were sampled from pet shops in four of the five municipalities in Gauteng Province, South Africa for genetic identification using mitochondrial cytochrome b (mtDNA) sequence data. Distance-based Neighbour-Joining (NJ), character-based maximum likelihood (ML) and model-based Bayesian inference (BI) were used to infer the relationship between the pet murid rodents. Brown rats (Rattus norvegicus) and house mice (Mus musculus) were the most dominant species in the pet shops. The results demonstrated that pet shop owners lacked the taxonomic expertise to identify murid rodent species they trade in. For example, the juveniles of brown rats were misidentified as adults of the house mouse. The murid rodents sampled in the current study were genetically affiliated to both wild and laboratory strains of R. norvegicus and M. musculus. The results of the BI showed that the pet murid rodents were in the terminal clades as those of conspecifics in NCBI GenBank reference sequences. The molecular data used in the current study may be useful for developing national policies and regulations for synanthropic invasive murid rodents in the pet trade industry in South Africa.