Abstract The use of more than one nomenclatural code is becoming increasingly common in some biological sub-disciplines. To minimize nomenclatural instability, we have decided to establish a higher level systematization for Thalattosuchia under both the International Code of Phylogenetic Nomenclature (‘PhyloCode’) and the International Code of Zoological Nomenclature (‘Zoological Code’). We undertook a series of phylogenetic analyses with an expanded dataset to examine the origins of Thalattosuchia within Crocodylomorpha, and determined the clade’s diagnostic characters. Based on these analyses, we provide updated diagnoses for Thalattosuchia and its subclades under both the PhyloCode and Zoological Code. We also introduce two new nomina that are regulated under the PhyloCode (Neothalattosuchia and Euthalattosuchia), and the nomen Dakosaurina, which is registered under both nomenclatural codes. Moreover, we introduce PhyloCode-compliant phylogenetic definitions for Thalattosuchia and its subclades. As we cannot reliably discriminate between the positional hypotheses for Thalattosuchia within Crocodylomorpha, the clades’ origins are as much of a mystery today as they were over a century ago. However, we hope that using the same diagnostic characters to define the same clades, with the same nomina, under both nomenclatural codes will be an example to others to follow.