The freshwater calanoid copepod Skistodiaptomus pallidus (Herrick, 1879), native to the Mississippi basin of North America, has recently established non-indigenous populations in New Zealand, Germany and Mexico. We used the mitochondrial cytochrome c oxidase subunit I (COI) gene to more precisely identify the origins of S. pallidus populations within New Zealand and Germany. The S. pallidus COI sequences suggested that both New Zealand and German populations were most similar to those from the most easterly regions of the USA (e.g., New York, Virginia and Georgia). However, several haplotypes were found to be divergent between the New Zealand and German populations, indicating the exact sources of the introductions were likely different for each country. German sequences possessed two of the major haplotypes known from the east coast of USA, while New Zealand had one, indicating a shipping related vector of introduction with greater propagule supplies to Germany is plausible. Although both German and New Zealand populations contained haplotypes identical to common east coast North American sequence records, both non-indigenous populations had haplotypes not yet recorded in the USA. Further sampling of the native range will be required to determine the exact origin of the non-indigenous S. pallidus populations and may also help to identify more precisely the vectors and pathways of the translocations.