Hybridization is particularly widespread in birds and can affect species status and recovery. The common quail Coturnix coturnix is a protected game species that has undergone significant population decrease due to habitat changes. The release of Japanese quail C. japonica and or hybrids for restocking has been occurring since the 1970’s. Both species have not developed reproductive isolating mechanisms and hybridization is occurring. Species distinction based on morphology and male callings is difficult. In this work cytochrome b gene and five microsatellite loci were used with the aim of establishing an identification test for quails sampled in Portugal. Cytochrome b gene revealed to be of promising use to identify the quail maternal lineage. Success in species assignment with the studied microsatellite loci was moderate to identify samples with suspicion of being hybrids with common quail maternal lineage.