The morphological data consists of ommatidial structures (see arthropod eye), the presence of neuroblasts, and the form and style of axonogenesis by pioneer neurons.

[11][12] In a 2005 study of nuclear genomes Regier et al. suggest that Hexapoda is most closely related to Branchiopoda and Cephalocarida + Remipedia, thereby hexapods are "terrestrial crustaceans", thus supporting the Pancrustacea hypothesis that maxillopods are not monophyletic (in the following cladograms Maxillopoda subclasses are highlighted).

[14] In 2013 combined study of morphology, including fossils, and molecular data, including expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data Oakley et al. obtained support for three pancrustacean clades: Oligostraca (Ostracoda, Mystacocarida, Branchiura, Pentastomida), Multicrustacea (Copepoda, Thecostraca, Malacostraca) and a clade they refer to as Allotriocarida (Branchiopoda, Cephalocarida, Remipedia, Hexapoda), as well as for monophyly of Ostracoda.

Relations within Allotriocarida remain uncertain: sister taxon to Hexapoda is either Remipedia, or the clade Branchiopoda + Cephalocarida, however, authors are inclined to the first version (see "Conclusion", 4), which is also consistent with von Reumont et al. (2012) results.

The discrepancy between the nucleotide-based and the amino acids-based trees is caused by substitutions within synonymous codon families (especially those of serine-TCN and AGY): different arthropod lineages are differentially biased in their usage of serine, arginine, and leucine synonymous codons, and the serine bias is correlated with the topology derived from the nucleotides, but not the amino acids.

Most of the inferences based on amino acids sequences support a clade which includes Branchiopoda, Remipedia, Copepoda and Hexapoda (group A).

Hexapoda Branchiopoda Remipedia Copepoda Thecostraca and Tantulocarida Malacostraca Oligostraca Cephalocarida Myriapoda The relationship of Hexapoda and the crustacean classes is shown in the following phylogenetic tree, which shows Allotriocarida, along with Oligostraca and Multicrustacea, as the three main divisions of subphylum Pancrustacea, embracing the traditional crustaceans and the hexapods (including insects).