The two-volume set, CCIS 681 and CCIS 682, constitutes the proceedings of the 11th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2016, held in Xi'an, China, in October 2016. The 115 revised full papers presented were carefully reviewed and selected from 343 submissions. The papers of Part I are organized in topical sections on DNA Computing; Membrane Computing; Neural Computing; Machine Learning. The papers of Part II are organized in topical sections on Evolutionary Computing; Multi-objective Optimization; Pattern Recognition; Others.