Brachiopods belonging to order Atrypida originated in the Middle Ordovician and went extinct in the Late Devonian. Few cladistic studies have been undertaken for this group. Here we investigate their early evolution through Silurian time. We present a parsimony-based phylogenetic analysis of 41 characters and 70 genera representing all the early taxonomic groups within the order. The stratigraphical record of the fossil genera analysed strongly aligns with the phylogeny recovered from our parsimony analysis. Most currently recognized subfamilies and families may be identified within clades, except for the Atrypinae, Idiospirinae, and the Septatrypidae. This warrants subdivision of the former and redefinition of the latter two. The subfamily Atrypinae is redefined, and a new subfamily of the Atrypidae, the Protatrypinae, is split off. Tracing character evolution across the tree indicates that the calcified spiralia and a jugum or jugal processes characterize all members of the Atrypida, except the most basal clade, the Cyclospiridae, which lacks a calcified jugum. Ribs are a homoplasious character, occurring in numerous clades throughout the tree. Darriwillian through Sandbian ages represent times with rapid evolution when most new autapomorphies seen in the atrypides evolved. This interval is the first major part of the Great Ordovician Biodiversification Event (GOBE). Solid teeth, dorsal direction of spiralia, elaborate ornamentation, and frills evolved in the latest Katian into early Silurian time. Solid teeth seen in distantly related clades from latest Katian onwards may be an analogous feature. The Late Ordovician Mass Extinction (LOME) is indicated in the stratigraphical tree together with a possible event at the end of the Aeronian. The tree supports the long-held assumptions that the Plectatrypinae evolved from the Spirigerininae. It further suggests that the genus Tuvaella may be included with the Davidsonioidea. Likewise, the redefined Atrypinae is a sister group of the Lissatrypidae and a derived group in the phylogenetic tree.