[2] Luis Chiappe later defined Pygostylia as a node-based clade, "the common ancestor of the Confuciusornithidae and Neornithes plus all its descendants".

Cladogram following the results of a phylogenetic study by Jingmai O'Connor and colleagues in 2016:[1] †Confuciusornithiformes †Didactylornis †Sapeornis Ornithothoraces In 2023, Li et al recovered their new taxon, Cratonavis, as the new jinguofortisid that belongs to Pygostylia.

The results of their phylogenetic analyses are shown in the cladogram below:[8] †Archaeopteryx †Jeholornis †Sapeornis Jinguofortis Cratonavis Chongmingia †Confuciusornithidae Ornithuromorpha † Enantiornithes Pygostylia has been recovered as being within the clade Avebrevicauda.

The group was named in 2002 by Gregory S. Paul to distinguish short-tailed avialans from their ancestors, such as Archaeopteryx, which had long, reptilian tails.

The earliest known member of the group is the enantiornithine species Protopteryx fengningensis, from the Sichakou Member of the Huajiying Formation of China, which dates to around 131 Ma ago,[10] though at least one other enantiornithine, Noguerornis, may be even older, at up to 145.5 million years ago, though its exact age is uncertain.