Interspecies hybridization is of concern for the management of invasive species, as it can allow the exchange of advantageous alleles between introduced species and undermine control efforts. In this study, hybridization between populations of introduced common carp and goldfish in Australia is investigated. Common carp and goldfish were sampled extensively from the Murray-Darling Basin, the largest river basin in Australia. Fish identified in the field as hybrids, on the basis of having truncated or missing pairs of barbels around their mouths, were also sampled. All fish were genotyped for five microsatellite loci that could be amplified through polymerase chain reaction in both species, and the mitochondrial DNA control region was sequenced in the field-identified hybrids and a subset of the goldfish and common carp. Bayesian clustering analyses, factorial correspondence analysis and direct inspection of the microsatellite profiles confirmed that all fish identified as hybrids in the field had ancestry from both species. A number of cryptic hybrids were also identified. While most hybrids were inferred to be F1-generation, some F2-generation and backcrossed individuals were detected, indicating that gene flow is ongoing between carp and goldfish in Australia. Gene flow was biased in favor of male carp mating with female goldfish, as 19 of the 20 F1-generation hybrids had goldfish maternal ancestry. This ongoing gene flow could allow advantageous alleles (e.g. resistance to koi herpes virus) to move between species. This study illustrates that invasive species control programs should not only target the species considered most destructive, but should also consider the risks posed by introgression with related species.