Fusarium sp. produces various bioactive pigments widely used in pharmaceuticals, cosmetics, and the food industry. This study investigated the antimicrobial effect of the pigment produced from the highest pigment-producing Fusarium sp. strain and determined the optimum growth conditions and agro-industrial residues to obtain maximum pigment production. Fusarium equiseti, Fusarium graminearum, and Fusarium poae strains were tested in terms of their pigment production levels. Pigment quantification was assessed by a UV–Visible Spectrophotometer at 500 nm. Antimicrobial tests were determined by Disc Diffusion and Well Diffusion Methods. According to our results, the highest amount of pigment-producing strain was F. graminearum (p<0.001) and malt extract broth (MEB) was the optimum growth media (p<0.001). Extracted F. graminearum pigment was antimicrobial against B. cereus and S. aureus with a zone of inhibition diameters of 10.2 and 14.9 mm respectively. Initial pH levels of 8, 150 rpm rotation speed, 30 ºC temperature, and 9 days of incubation under the light condition in MEB media were determined as the optimum growth conditions for the highest reddish pigment production. Moreover, 10-2 times diluted molasses, Turkish feta cheese whey, and Turkish cheddar cheese whey were found as suitable low-cost growth media for reddish pigment production by F. graminearum. Our findings not only represent a pigment that might be used in the food industry as an antimicrobial bio-colorant but also show the potential use of molasses and whey as low-cost growth media for reddish pigment production by F. graminearum.