Citromycin is widely used in the pharmaceutical industry due to its potent antimicrobial properties. It is primarily applied in the treatment of bacterial infections, especially those caused by gram-positive organisms. Its effectiveness in inhibiting protein synthesis in bacteria makes it a valuable component in broad-spectrum antibiotic formulations.

In veterinary medicine, Citromycin is used to manage respiratory, urinary, and skin infections in livestock and companion animals. It is often administered orally or through injection, depending on the formulation and target species.

The compound also finds application in agriculture as a growth promoter and disease preventive agent in poultry and aquaculture. However, its use is regulated to prevent antibiotic resistance development.

Additionally, Citromycin is utilized in research settings for microbial selection in cell culture and genetic engineering, particularly in plasmid maintenance where resistance genes are employed as markers.