Protein metabolism in skin and muscle was studied in Merino wethers selected for high (F+, n = 10) or low (F–, n = 10) estimated breeding values for clean fleece weight, but with similar estimated breeding values for liveweight and fibre diameter, raised to 20 months of age under the same conditions, and then offered two levels of nutrition (0.8 or 1.8 × maintenance) for 37 days. Over 37 days, F+ sheep had greater rate of wool production, liveweight gain, and had greater eye-muscle and fat depth than F– sheep (P < 0.05). Fractional synthesis rates of protein (%/day) in the epidermis, dermis, whole skin and muscle were affected by both feeding level (P < 0.05) and genotype (P < 0.05). The fractional synthesis rates of protein were greater (P < 0.05) in F+ sheep at both levels of intake. There was an interaction (P < 0.01) between genotype and feeding level for the protein fractional synthesis rate in muscle, where F+ sheep were more responsive to higher feed intake. Muscle of F– sheep responded to increased amino acid supply by reducing the rate of protein degradation without altering synthesis rate; whereas muscle of F+ sheep responded by increasing the rates of both protein synthesis and degradation. The overall muscle fractional synthesis rate (1.6%/day) was ~7-times lower than the skin fractional synthesis rate (10.8%/day) in these animals (P < 0.01). F+ sheep had a higher rate of protein synthesis in dermis and whole skin to support their higher wool protein accretion at both levels of feed intake. Muscle protein synthesis rate was greater in F+ sheep offered above-maintenance metabolisable energy (ME) intake than those given below-maintenance ME intake but was unaffected by ME intake in F– sheep. The results indicate that selection for wool growth not only affects production of wool and the wool follicle, but also affects the rate of protein turnover in components of the skin and skeletal muscle.