This two-volume set LNCS 16011 and 16012 constitutes the refereed post-conference proceedings of the 16th International Conference on Advances in Swarm Intelligence, ICSI 2025, held in Yokohama, Japan, during July 11-15, 2025. The 54 revised full papers presented in these proceedings were carefully reviewed and selected from 116 submissions. The papers are organized in the following topical sections: Particle Swarm Optimization; Swarm Optimization Algorithms; Swarm of Large Language Models; Agent and Multi-agents; Vehicle Routing; Multiobjective Optimization; Approaches for Classification and Feature Selection; Prediction and Detection Algorithms; Machine Learning.