The inadequately controlled trade in gyr and saker falcons has lead to saker falcons becoming endangered and both species being CITES listed. However, the phylogenetic relationship between these nominal species is unresolved preventing their molecular identification and limiting the availability of data for conservation management. This study amplified DNA from the mitochondrial cytochrome oxidase I (COI) gene and nine nuclear microsatellite markers to highlight previously unobserved genetic differences between these two putative species. Results show that gyr and saker are paraphyletic using COI and therefore indistinguishable using this marker. However, the microsatellite allele frequency differences suggest that it is possible to assign an unidentified bird to its correct species with 98% accuracy. The results suggest the two species should be monitored separately to ensure short term conservation success.