In this study, utilization of whey and grape must were investigated for citric acid production using Yarrowia lipolytica NBRC 1658 and a domestic strain Y. lipolytica 57. In addition to its use as a sole nutrient source, whey was also fortified with glucose or fructose as well as other nutrients. The best results for citric acid production were obtained in the medium containing whey supplemented with fructose. Maximum citric acid concentrations in this medium were 49.23 and 32.65 g/L for the domestic and NBRC 1658 strains, respectively. In grape must, maximum citric acid concentrations obtained using domestic and NBRC 1658 strains were 32.09 and 10.39 g/L, respectively. Both of the natural nutrient sources were found to be promising for utilization in citric acid production process. A domestic Turkish yeast strain was confirmed to be superior for citric acid production for the first time. This can be targeted for enhancing citric acid production efficiencies from locally available substrates such as whey or grape must.