There is much speculation about the origin and phylogeny of tapeworms. One evolutionary scheme proposes that they arose from a stock of aquatic, free-living, bottom-dwelling proto-monogeneans that, in turn, evolved from a rhabdocoel-like ancestor similar to the ancestral form suggested for digeneans. The immediate ancestors of modern tapeworms evolved adhesive organs that enabled them to become attached to, and subsequently ectoparasitic upon, bottom-dwelling vertebrates. Some of these ectoparasitic forms migrated internally to the gut of these vertebrates and became endoparasitic. To survive in this hostile environment, these organisms evolved protective modifications, such as a glycocalyx on the body surface and resistant, quinone-tanned eggshells. Such modifications enabled them to resist the actions of the hosts' digestive enzymes.

They also underwent physiological adaptations that allowed them to survive in an environment with reduced oxygen tension. At least one branch of these animals evolved additional modifications, such as the loss of the gut, development of anterior attachment organs, and duplication of reproductive systems, the latter leading eventually to strobilization. Later modifications, as the group became increasingly diverse, included adoption of intermediate hosts and the appearance of apolysis, the release of gravid proglottids to the exterior. A causal relationship appears certain between the development of apolysis and the loss of capacity to form resistant eggshells by tanning (resulting in loss of protection from host digestive enzymes), although there is a "chicken or egg" kind of question as to which occurred first.