The melatonin receptor 1A (MTNR1A) and inhibin alpha subunit (INHA) genes play a significant role in the reproductive characteristics of animals. Blood samples were collected from 371 goats (Honamli and Hair) reared in Antalya and Burdur. The polymerase chain reaction (PCR) products were digested by RsaI for the MTNR1A gene and HaeII for the INHA gene. Two alleles (A and G) and three genotypes (AA, AG, and GG) were observed for the INHA gene, while two alleles (R and r) and two genotypes (RR and Rr) were observed for the MTNR1A gene. The highest allelic frequency value for G (91.8%) was found in Honamli goat breeds for the INHA gene while the highest value for R (98.1%) was found in Hair goat breeds for the MTNR1A gene. The GG genotype for the INHA gene and the RR genotype for the MTNR1A gene were identified as the most common genotypes of the Honamli and Hair goat breeds. The rr genotype for the MTNR1A gene could not be determined in the breeds. Both Honamli and Hair goat breeds were in Hardy-Weinberg equilibrium for the genes that were studied. In conclusion, this study confirms the existence of genetic polymorphism in the MTNR1A and INHA genes as detected by PCR-RFLP analysis in Honamli and Hair goat breeds.