The aim of this study was to investigate the restriction fragment length polymorphism (RFLP) of some loci on chromosomes 1 (CJA1) and 3 (CJA3) in Japanese quails (Coturnix coturnix japonica) raised in Turkey. With this study population genetics parameters were estimated in order to select individuals for establishing a reference population, which would be used for studies on recombination frequency. Fertilized eggs obtained from flocks raised in six different provinces of Turkey were incubated for 120 h and 191 embryos were collected. From the tissue samples of the embryos, DNA was isolated by using DNA isolation kits. Particular regions of SEMA3E, IFR1, HAL, LOC396025, UGP2, LOC396192, TLX and BMP5 loci were amplified with specifically designed primers for each locus by using PCR technique. The PCR products were cut with an appropriate restriction enzyme for each locus and analysed by using agarose gel electrophoresis. Presence of different alleles, allele and genotype frequencies, heterozygosities and genetic distances were estimated. Out of the eight loci studied, polymorphism was found for the SEMA3E and TLX loci on 1. and 3. chromosomes, respectively, while five loci were found to be monomorphic and one locus (HAL) could not be amplified by PCR. The populations studied were found to be mostly in Hardy-Weinberg equilibrium. The results indicated that the SEMA3E and TLX loci can be used for studying recombination frequencies in the populations included into the study.