The major subdivisions among the Archaeocyatha are based on early ontogenetic features. Lower taxonomic categories are determined by characters exhibited later in development. Accordingly, the two main groups of Archaeocyatha, the Regulares and the Irregulares are distinguished on the basis of presence or absence of a character expressed in the very earliest stage of growth. Similarly, superfamilies and families are based on outer and inner wall characters, respectively. This results in a neat classification scheme, though it probably does not approximate the phylogenetic history of the group. By the current scheme, the phylum Archaeocyatha is split into two classes, six orders, 12 suborders, 120 families and nearly 300 genera.
It is probable that the Archaeocyatha is a clade nested within the Porifera. Archaeocyath organization is consistent with that of living sponges. The one phylogenetic analysis (carried out by Reitner) that included archaeocyaths with other sponges, grouped them as sisters to the demosponges. Therefore, although the taxonomic term Archaeocyatha is often accorded phylum status, this violates the taxonomic ranking system.