Brilliant green is widely used as a dye in microbiology for staining purposes, particularly in the preparation of selective media to isolate and identify bacteria. It inhibits the growth of gram-positive bacteria, making it useful for differentiating bacterial species in clinical and environmental samples.

In histology, it is employed as a biological stain to highlight specific structures in tissue samples under microscopic examination. Additionally, it has applications in the textile industry for dyeing fabrics, providing a vibrant green color.

In aquaculture and fisheries, brilliant green is used as an antifungal agent to treat infections in fish and fish eggs, helping to improve survival rates. Its antiseptic properties also make it suitable for topical use in veterinary medicine to treat minor wounds and infections in animals.