This book constitutes the proceedings of the 9th International Conference on Similarity Search and Applications, SISAP 2016, held in Tokyo, Japan, in October 2016. The 18 full papers and 7 short papers presented in this volume were carefully reviewed and selected from 47 submissions. The program of the conference was grouped in 8 categories as follows: graphs and networks; metric and permutation-based indexing; multimedia; text and document similarity; comparisons and benchmarks; hashing techniques; time-evolving data; and scalable similarity search.