The Fregatidae (frigatebirds), Sulidae (gannets and boobies), Phalacrocoracidae (cormorants and shags), Anhingidae (darters), and Phaethontidae (tropicbirds) were traditionally placed in the Pelecaniformes, but molecular and morphological studies indicate they are not such close relatives.

[4] Sibley and Ahlquist's landmark DNA-DNA hybridisation studies (see Sibley-Ahlquist taxonomy) led to them placing the families traditionally contained within the Pelecaniformes together with the grebes, cormorants, ibises and spoonbills, New World vultures, storks, penguins, albatrosses, petrels, and loons together as a subgroup within a greatly expanded order Ciconiiformes, a radical move which by now has been all but rejected: their "Ciconiiformes" merely assembled all early advanced land- and seabirds for which their research technique delivered insufficient phylogenetic resolution.

Morphological study has suggested pelicans are sister to a gannet-cormorant clade, yet genetic analysis groups them with the hamerkop and shoebill, though the exact relationship between the three is unclear.

[6] Reviewing genetic evidence to date, Cracraft and colleagues surmised that pelicans were sister to the shoebill with the hamerkop as the next earlier offshoot.

[7] Ericson and colleagues sampled five nuclear genes in a 2006 study spanning the breadth of bird lineages, and came up with pelicans, shoebill and hamerkop in a clade.

This is "Sula" ronzoni from Early Oligocene rocks at Ronzon, France, which was initially believed to be a sea-duck and possibly is an ancestral Pelecaniform.

Of those apparently basal taxa, the following show some similarities to the traditional Pelecaniformes: The proposed Elopterygidae—supposedly a family of Cretaceous Pelecaniformes—are neither monophyletic nor does Elopteryx appear to be a modern bird.