This book constitutes the refereed proceedings of the 9th International Workshop on Algorithms in Bioinformatics, WABI 2009, held in Philadelphia, USA, in September 2009. The 34 revised full papers presented together with the abstract of a keynote talk were carefully reviewed and selected from 90 submissions. All current issues of algorithms in bioinformatics are addressed, reaching from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. The topics range in biological applicability from gene interaction networks, molecular phylogeny, RNA and protein structure, and genome evolution.