The Pterosauria is an enigmatic group of volant reptiles from the Mesozoic. Despite demonstrating conspicuous apomorphic conditions, including an enlarged humeral deltopectoral crest, elongate wing spar comprising the fourth manual digit, and unique skull bone configurations, their cladogenesis is uncertain. While the ingroup monophyly of Pterosauria is clear, their interrelationships are contentious. The earliest studies of pterosaur phylogeny were concerned with phenotypic groups. The earliest cladistic analyses of pterosaurs in the late 20th Century were simple and were superseded by more comprehensive analyses in the early 21st Century. These analyses are comparable at the genus, family, and suborder level, but the ranks between these are incongruent between authors, leading to nomenclatural disputes. This study aims to understand the differences that exist between the competing phylogenetic hypotheses, why they exist, and to establish a more robust phylogenetic hypothesis. An extensive review of pterosaur phylogeny, cladistic character coding, and data transformation is performed. A distinct cladistic analysis is developed independently of the literature, providing a reference tree for a meta-analysis of topological congruence. Furthermore, this distinct analysis is supplemented with published characters to produce a comprehensive analysis which is a robust hypothesis of pterosaur phylogeny. Taxonomic actions are taken on the wastebasket taxon Pterodactylus and the paraphyletic genus Germanodactylus, to improve the taxonomic content of the analyses. The results demonstrate that analyses sharing characters produce trees with greater levels of congruence. Although this may be due to the introduction of biases, it is far more likely that the improvement seen in the comprehensive tree at least, is due to improving the phyletic content, sampling of anatomy, and reducing the negative effects of homoplasy. This is supported by the comprehensive tree's congruence to the stratigraphic record. The comprehensive tree agrees with the common clades of other studies, but some families are found in unique positions, most notably the Anurognathidae.