This book constitutes the refereed proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching, CPM 2005, held in Jeju island, Korea on June 19-22, 2005. The 37 revised full papers presented were carefully reviewed and selected from 129 submissions. They constitute original research contributions in combinatorial pattern matching and its applications. Among the application fields addressed are computational biology, bioinformatics, genomics, proteinomics, data compression, Sequence Analysis and Graphs, information retrieval, data analysis, and pattern recognition.