The effect of β-lactoglobulin (<i>β-LG</i>) and κ-casein (<i>CSN3</i>) genotypes on milk composition were evaluated in Iranian indigenous Zel sheep breed. Genotypes were determined by PCR amplification followed by digestion with <i>RsaI</i> enzyme for exon II of the <i>β-LG</i> gene and SSCP method for exon IV of the <i>CSN3</i> gene. Polymorphism was detected in all PCR products. β-lactoglobulin showed two alleles and three genotypes and <i>CSN3</i> gene revealed two conformational patterns, respectively. Results indicated that there were significant associations between AB genotype of <i>β-LG</i> gene with higher fat and lactose percentages and also between K<sub>1</sub> pattern of <i>CSN3</i> gene with higher lactose percentage. Therefore, it is feasible to improve milk composition in Zel sheep breed using <i>β-LG</i> and <i>CSN3</i> genes.