Evolutionary relationships of fossil gastropods have largely been inferred using taxonomic systematics. Phylogenetic relationships between extinct gastropod groups and their relationship to extant groups are largely unresolved. Here we reconstruct the phylogeny of Pleurotomariida, which has the longest fossil record among extant gastropod clades and represents one of the most diverse Palaeozoic gastropod groups. Bayesian (fossilized birth–death [FBD] model) and parsimony analyses were performed using 93 morphological shell characters comprising 109 pleurotomariidan species representing 80 genera/subgenera ranging from the Ordovician to Recent. Parsimony analysis failed to reconstruct stratigraphically congruent trees and many nodes have poor support. The FBD model incorporates the stratigraphical ages of taxa for tree reconstruction and therefore better fits the stratigraphical record. According to the FBD phylogeny, Pleurotomariida was represented by three distinct lineages during the Palaeozoic: Eotomariini, Wortheniellini and Pleurotomariini. Pleurotomariini and Wortheniellini survived the end-Permian mass extinction. Although Wortheniellini showed a higher diversification during the Triassic recovery period, only Pleurotomariini survived until the present day, suggesting that resilience to extinction was not dependent on diversification dynamics in this clade. The FBD analysis indicates that groups that have an exclusively Triassic fossil record originated during the Permian and that the origination and extinction rates increased from the Ordovician to the Jurassic and dropped subsequently. Sampling standardized diversity analysis of Pleurotomariida corroborates that they were one of the most diverse gastropod groups in the late Palaeozoic and that their diversity significantly dropped after the end-Permian mass extinction. Early ontogenetic shell characters are more conservative (phylogenetically more informative) compared to late ontogenetic shell characters. In contrast to previous assumptions, axial characters are not more homoplastic than spiral shell characters, as indicated by higher consistency index values. The data further revealed that adult gastropod shell size depends significantly on the protoconch size and the initial whorl size.