Recombination is the major motor of evolution. While mutations result in gradual changes, recombination reshuffles entire functional modules and thus progresses evolution in leaps and bounds. We need to identify recombination breakpoints in sequences to understand the evolutionary process, the impact of recombination, and to reconstruct the phylogenetic history of genes and genomes. This chapter provides a step by step guide for detecting recombination even in large and complex sequence alignments.