The proximate and fatty acid composition of two locally important freshwater fish, Schizothorax zarudnyi and Schizocypris altidorsalis, from Sistan Province in Iran were investigated for their nutritional value. The protein and lipid content in the S. zarudnyi were 14.67 and 6.36%, respectively. In S. altidorsalis, protein and lipid content were 13.03 and 4.52%. There was quantitative difference between individual fatty acids of these two fish. Totally 18 fatty acids were found. In S. zarudnyi, DHA was the highest among the poly-unsaturated fatty acids with 42.85%, followed by EPA with 29.62% of the total poly-unsaturated fraction. In S. altidorsalis, EPA was the highest among the poly-unsaturated fatty acids with 45.05%, followed by DHA with 27.87% the total poly-unsaturated fraction. The n-6/n-3 ratio was 0.26 and 0.20 for S. zarudnyi and S. altidorsalis, respectively. High n-3 fatty acids content in these fish revealed that they have high nutritional value. Schizothorax zarudnyi showed better nutritional value in comparison to protein and lipid content of S. altidorsalis.