This book constitutes the proceedings of the Third International Conference on Algorithms for Computational Biology, AlCoB 2016, held in Trujillo, Spain, in June 2016. The 13 full papers presented in this volume were carefully reviewed and selected from 23 submissions. They are organized in the following topical sections: biological networks and modelling; biological structure processing; phylogenetics; and sequence analysis and rearrangement. In addition one invited talk is included.