This volume contains the papers presented at RECOMB 2009: the 13th Annual International Conference on Research in Computational Molecular Biology held in Tucson, Arizona, USA, during May 18-21, 2009. The RECOMB conference series was started in 1997 by Sorin Istrail, Pavel Pevzner, and Michael Wat- man. RECOMB 2009 was hosted by the University of Arizona, organized by a committeechairedbyJohnKececioglu, andtookplaceatTheWestinLaPaloma Resort and Spa in Tucson, Arizona. This year, 37 papers were acccepted for presentation out of 166 submissions. The papers presented were selected by the Program...