In their original usage, it was intended as a paraphyletic grouping that contained caenogastropods and non-euthyneuran heterobranchs.

[3][4][5] Phylogenetic analyses based on the mitochondrial genome have historically found Apogastropoda to be non-monophyletic,[6] but this is considered an artifact of long branch attraction and the reliability of the mitochondrial genome for resolving deep relationships in molluscs has been questioned.

[7] Early analyses of the mitogenome, which recovered Heterobranchia as the sister taxon of Patellogastropoda instead of Caenogastropoda, included data from only one patellogastropod taxon, Lottia digitalis, which has undergone a high rate of evolutionary change to its mitogenome that obscures its evolutionary relationships.

[3] Apogastropods are generally characterized by a single pair of head tentacles, each of which contains a nerve that is deeply forked into two parallel branches.

In euthyneurans, this condition is modified so that each nerve branch forms a separate tentacle.