This two-set volume LNCS 15756 and 15767 constitutes the refereed proceedings of the 21st International Symposium on Bioinformatics Research and Applications, ISBRA 2025, held in Helsinki, Finland, during August 3–5, 2025. The 66 full papers were carefully reviewed and selected from 167 submissions. This year’s symposium brought together leading researchers, scientists, and industry professionals from around the world to share cutting-edge advancements, foster collaboration, and explore the future of bioinformatics and computational biology.