This book constitutes the thoroughly refereed post-conference proceedings of the 16th Japanese Conference on Discrete and computational Geometry and Graphs, JDCDGG 2013, held in Tokyo, Japan, in September 2013. The total of 16 papers included in this volume was carefully reviewed and selected from 58 submissions. The papers feature advances made in the field of computational geometry and focus on emerging technologies, new methodology and applications, graph theory and dynamics.