1. Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. 2. Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. 3. popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining. 4. The software is open source and freely available for all major operating systems.