The aim of the present study was to optimize production conditions of yellow, orange and red pigments from the fungus Monascus ruber Went AUMC 5705 culture through submerged fermentation (SMF), then separation and application of the produced pigments individually in flavored yogurts. Maximum pigments productivity was achieved at incubation temperature of 30℃, inoculums size by 4% (V/V) with (36×104 spores /ml of inoculum), pH of 6.5 and incubation period of 11 days. The favorable carbon and nitrogen sources were Dextrin and monosodium glutamate at 4% (W/V) and 1.5% (W/V) concentrations respect. The present study has also revealed that the yogurt preparations supplemented with these pigments received highly acceptability. To the best of our knowledge, this is the first report on application of yellow, orange and red Monascus pigments individually in flavored yogurts. It is fervently hoped that in the future, these fungal pigments could receive greater attention in the field of food industries.