Proteolytic cascades play integral roles in immunity, inflammation, development and signalling. Serine protease inhibitors (serpins) are ubiquitous throughout nature and are the largest group of proteins that regulate such cellular processes. Despite interest since their discovery, a unified model that describes the functional divergence and taxonomic distribution of serpins has remained elusive. Here, we present a comprehensive phylogenomic analysis of the Serpin superfamily. Using recently developed phylogenetic methods, we are able to unify and resolve deep branches in the Serpin phylogeny that emphasize relationships in Serpin sequence, structure and function and reveal the molecular mechanisms of evolution that drive divergence within the superfamily. Interestingly – our results indicate that there has been extensive horizontal gene transfer throughout the Serpin superfamily, including rare transfer events from chordates to prokaryotic members of the commensal microbiome.