The cormorants are a group traditionally placed within the Pelecaniformes or, in the Sibley–Ahlquist taxonomy, the expanded Ciconiiformes.
This latter group is certainly not a natural one, and even after the tropicbirds have been recognised as quite distinct, the remaining Pelecaniformes seem not to be entirely monophyletic.
Their relationships and delimitation – apart from being part of a "higher waterfowl" clade which is similar but not identical to Sibley and Ahlquist's "pan-Ciconiiformes" – remain mostly unresolved.
Notwithstanding, all evidence agrees that the cormorants and shags are closer to the darters and Sulidae (gannets and boobies), and perhaps the pelicans or even penguins, than to all other living birds.

In recent years, three preferred treatments of the cormorant family have emerged: either to leave all living cormorants in a single genus, Phalacrocorax, or to split off a few species such as the imperial shag complex (in Leucocarbo) and perhaps the flightless cormorant.
Alternatively, the genus may be disassembled altogether and in the most extreme case be reduced to the great, white-breasted and Japanese cormorants.

Pending a thorough review of the Recent and prehistoric cormorants, the single-genus approach is followed here for three reasons: first, it is preferable to tentatively assigning genera without a robust hypothesis.
Second, it makes it easier to deal with the fossil forms, the systematic treatment of which has been no less controversial than that of living cormorants and shags.
Third, this scheme is also used by the IUCN, making it easier to incorporate data on status and conservation.
In accordance with the treatment there, the imperial shag complex is here left unsplit as well, but the king shag complex has been.

The cormorants and the darters have a unique bone on the back of the top of the skull known as the os nuchale or occipital style which was called a xiphoid process in early literature.
This bony projection provides anchorage for the muscles that increase the force with which the lower mandible is closed.
This bone and the highly developed muscles over it, the M. adductor mandibulae caput nuchale, are unique to the families Phalacrocoracidae and Anhingidae.

Several evolutionary groups are still recognizable.
However, combining the available evidence suggests that there has also been a great deal of convergent evolution; for example the cliff shags are a convergent paraphyletic group.
The proposed division into Phalacrocorax sensu stricto (or subfamily "Phalacrocoracinae") cormorants and Leucocarbo sensu lato (or "Leucocarboninae") shags does indeed have some degree of merit.
The resolution provided by the mtDNA 12S rRNA and ATPase subunits six and eight sequence data is not sufficient to properly resolve several groups to satisfaction; in addition, many species remain unsampled, the fossil record has not been integrated in the data, and the effects of hybridisation – known in some Pacific species especially – on the DNA sequence data are unstudied.
The cormorants are a group traditionally placed within the Pelecaniformes or, in the Sibley–Ahlquist taxonomy, the expanded Ciconiiformes. This latter group is certainly not a natural one, and even after the tropicbirds have been recognised as quite distinct, the remaining Pelecaniformes seem not to be entirely monophyletic. Their relationships and delimitation – apart from being part of a "higher waterfowl" clade which is similar but not identical to Sibley and Ahlquist's "pan-Ciconiiformes" – remain mostly unresolved. Notwithstanding, all evidence agrees that the cormorants and shags are closer to the darters and Sulidae (gannets and boobies), and perhaps the pelicans or even penguins, than to all other living birds.
In recent years, three preferred treatments of the cormorant family have emerged: either to leave all living cormorants in a single genus, Phalacrocorax, or to split off a few species such as the imperial shag complex (in Leucocarbo) and perhaps the flightless cormorant. Alternatively, the genus may be disassembled altogether and in the most extreme case be reduced to the great, white-breasted and Japanese cormorants.
Pending a thorough review of the Recent and prehistoric cormorants, the single-genus approach is followed here for three reasons: first, it is preferable to tentatively assigning genera without a robust hypothesis. Second, it makes it easier to deal with the fossil forms, the systematic treatment of which has been no less controversial than that of living cormorants and shags. Third, this scheme is also used by the IUCN, making it easier to incorporate data on status and conservation. In accordance with the treatment there, the imperial shag complex is here left unsplit as well, but the king shag complex has been.
The cormorants and the darters have a unique bone on the back of the top of the skull known as the os nuchale or occipital style which was called a xiphoid process in early literature. This bony projection provides anchorage for the muscles that increase the force with which the lower mandible is closed. This bone and the highly developed muscles over it, the M. adductor mandibulae caput nuchale, are unique to the families Phalacrocoracidae and Anhingidae.
Several evolutionary groups are still recognizable. However, combining the available evidence suggests that there has also been a great deal of convergent evolution; for example the cliff shags are a convergent paraphyletic group. The proposed division into Phalacrocorax sensu stricto (or subfamily "Phalacrocoracinae") cormorants and Leucocarbo sensu lato (or "Leucocarboninae") shags does indeed have some degree of merit. The resolution provided by the mtDNA 12S rRNA and ATPase subunits six and eight sequence data is not sufficient to properly resolve several groups to satisfaction; in addition, many species remain unsampled, the fossil record has not been integrated in the data, and the effects of hybridisation – known in some Pacific species especially – on the DNA sequence data are unstudied.
Cormorant