This book constitutes the refereed proceedings of the Second International Conference on Combinatorial Optimization and Applications, COCOA 2008, held in St. John's, Canada, in August 2008. The 44 revised full papers were carefully reviewed and selected from 84 submissions. The papers feature original research in the areas of combinatorial optimization -- both theoretical issues and and applications motivated by real-world problems thus showing convincingly the usefulness and efficiency of the algorithms discussed in a practical setting.