Isoxanthopterin is primarily utilized in biochemical research as a fluorescent marker. Its ability to emit fluorescence under specific conditions makes it valuable for tracking and visualizing biological processes in cellular studies. Researchers employ it to study enzyme activities, particularly those involving pteridine metabolism, and to monitor cellular responses in various experimental setups. Additionally, it serves as a reference compound in analytical chemistry for identifying and quantifying related pteridine derivatives in biological samples. Its unique fluorescence properties also contribute to its use in developing biosensors and diagnostic tools for detecting specific biochemical interactions.