The purpose of this study was to identify mutations in melatonin receptor 1A (MTNR1A) and aromatase cytochrome P450 (CYP19) genes using PCR-RFLP technique and their associations with sperm quality and testicular size traits in Sanjabi breed rams. The blood and sperm samples were collected from Sanjabi rams (n = 96). Genomic DNA was extracted from the blood. A 824bp fragment from exon II of MTNR1A gene and a 517bp fragment from promoter 2 (P2) of CYP19 gene were amplified using two pairs of specific primers. The PCR products were separately digested by two restriction enzymes, SsiI for MTNR1A locus and DraI for CYP19 locus. Digestion by SsiI restriction enzyme resulted in CC, CA and AA genotypes with frequency of 0.45, 0.41 and 0.14, respectively. However, digestion of 517bp fragment of CYP19 gene by DraI endonuclease determined two AG and AA genotypes with frequency 0.89 and 0.11, respectively. The Chi-square test proved that the two loci were in Hardy-Weinberg equilibrium (HWE). The significant effect was observed between different genotypes of MTNR1A gene and morphological trait (P<0.05) and there was a significant association between different genotypes of CYP19 gene and scrotal circumference trait (P<0.05). The results of this study indicated that polymorphisms of MTNR1A and CYP19 genes were not associated with most traits of sperm quality and testicular sizes. Therefore, it seems that further studies are needed to identify mutations in other regions of these genes and other genes responsible to genomic regions for the sperm quality and testicular size in Sanjabi ram in order to improve fertility in these herds.