A revised hypothesis for the phylogeny of the Subclass Polyonchoinea (Monogenoidea) was constructed employing phylogenetic systematics. The Acanthocotylidae (formerly of the Order Capsalidea) is transferred to the Order Gyrodactylidea based on this analysis. The new phylogeny is used to determine coevolutionary relationships of the familial taxa of Monogenoidea with their hosts. The coevolutionary analysis suggests that the Monogenoidea apparently underwent sympatric speciation or dispersal while parasitic on ancestral Gnathostomata, resulting in two primary clades: the Polyonchoinea and the Oligonchoinea + Polystomatoinea. The two parasite clades apparently cospeciated independently with divergence of the Chondrichthyes and Osteichthyes. In the Polyonchoinea, the clade associated with Chondrichthyes experienced primary extinction within the Holocephala, but coevolved into the Loimoidae and Monocotylidae in the Galeomorphii and Squalea (Elasmobranchii), respectively. Within the Osteichthyes, polyonchoineans experienced primary extinction with the divergence of Sarcopterygii, Polypteriformes and Acipenseriformes. They demonstrate primary dispersal from the Neopterygii into the Squalea (as Amphibdellatinea), Actinistia (as Neodactylodiscinea) and Urodela (as Lagarocotylidea). Secondary dispersals of polyonchoineans occurred in the Gyrodactylidae to the Polypteriformes, Urodela and Anura; in the Acanthocotylidae to the Myxinoidea and Squalea; in the Capsalidae to the Acipenseriformes and Elasmobranchii; and in the Monocotylidae to the Holocephala. The Oligonchoinea and Polystomatoinea developed upon divergence of the Chondrichthyes and Osteichthyes. Oligonchoineans cospeciated within the Chondrichthyes, with the Chimaericolidea developing within the Holocephala and the ancestor of the Diclybothriidea + Mazocraeidea within the Elasmobranchii. Two cases of primary dispersal occurred within this clade: the Diclybothriidae to the Acipenseriformes and the ancestor of mazocraeidean families to the Neopterygii (both Osteichthyes). Secondary dispersal within the Oligonchoinea includes host switching of the common ancestor of Callorhynchocotyle (Hexabothriidae) to the Holocephala. Polystomatoineans coevolved within the Osteichthyes, but experienced primary extinctions in the Actinopterygii, Actinistia, Dipnoi and Amniota. Coevolution of the Sphyranuridae and Polystomatidae occurred with divergence of the Urodela and Anura, respectively. Secondary dispersal of Polystomatids to the Urodela, Dipnoi and Amniota is suggested. A preliminary phylogenetic analysis of the Polystomatoinea suggests that primary extinction with secondary dispersal of polystomatids to the Dipnoi may not be necessary to explain extant parasite distributions, since Concinnocotyla (Concinnocotylinae) appears to represent the sister taxon of the remaining Polystomatidae + Sphyranuridae.