Spectinomycin dihydrochloride is primarily used as an antibiotic in both human and veterinary medicine. It is effective against a variety of bacterial infections, particularly those caused by Gram-negative and Gram-positive bacteria. In humans, it is commonly prescribed for the treatment of gonorrhea, especially in cases where the infection is resistant to other antibiotics like penicillin. It works by inhibiting bacterial protein synthesis, thereby stopping the growth and spread of the bacteria.

In veterinary medicine, it is used to treat respiratory and gastrointestinal infections in animals, including poultry, cattle, and swine. It is often administered via injection or added to drinking water to ensure effective delivery. Additionally, it is sometimes used in aquaculture to control bacterial infections in fish.

The compound is also utilized in research settings as a selective agent in molecular biology experiments, particularly in the cultivation of genetically modified organisms. Its ability to inhibit bacterial growth makes it a valuable tool for ensuring the purity of cell cultures and for selecting cells that have been successfully transformed with specific genetic markers.