structural:expansion, structural:reformatting
Evolution and fossil record

The details of the evolution of the cormorants are mostly unknown. Even the technique of using the distribution and relationships of a species to figure out where it came from, biogeography, usually very informative, does not give very specific data for this probably rather ancient and widespread group. However, the closest living relatives of the cormorants and shags are the other families of the suborder Sulae — darters and gannets and boobies —which have a primarily Gondwanan distribution. Hence, at least the modern diversity of Sulae probably originated in the southern hemisphere.

While the Leucocarbonines are almost certainly of southern Pacific origin—possibly even the Antarctic which, at the time when cormorants evolved, was not yet ice-covered—all that can be said about the Phalacrocoracines is that they are most diverse in the regions bordering the Indian Ocean, but generally occur over a large area.

Similarly, the origin of the family is shrouded in uncertainties. Some Late Cretaceous fossils have been proposed to belong with the Phalacrocoracidae: A scapula from the Campanian - Maastrichtian boundary, about 70 mya (million years ago), was found in the Nemegt Formation in Mongolia; it is now in the PIN collection. It is from a bird roughly the size of a spectacled cormorant, and quite similar to the corresponding bone in Phalacrocorax. A Maastrichtian (Late Cretaceous, c. 66 mya) right femur, AMNH FR 25272 from the Lance Formation near Lance Creek, Wyoming, is sometimes suggested to be the second-oldest record of the Phalacrocoracidae; this was from a rather smaller bird, about the size of a long-tailed cormorant. However, cormorants likely originated much later, and these are likely misidentifications.

As the Early Oligocene "Sula" ronzoni cannot be assigned to any of the sulid families—cormorants and shags, darters, and gannets and boobies—with certainty, the best interpretation is that the Phalacrocoracidae diverged from their closest ancestors in the Early Oligocene, perhaps some 30 million years ago, and that the Cretaceous fossils represent ancestral sulids, "pelecaniforms" or "higher waterbirds"; at least the last lineage is generally believed to have been already distinct and undergoing evolutionary radiation at the end of the Cretaceous. What can be said with near certainty is that AMNH FR 25272 is from a diving bird that used its feet for underwater locomotion; as this is liable to result in some degree of convergent evolution and the bone is missing indisputable neornithine features, it is not entirely certain that the bone is correctly referred to this group.

Phylogenetic evidence indicates that the cormorants diverged from their closest relatives, the darters, during the Late Oligocene, indicating that most of the claims of Cretaceous or early Paleogene cormorant occurrences are likely misidentifications.

During the late Paleogene, when the family presumably originated, much of Eurasia was covered by shallow seas, as the Indian Plate finally attached to the mainland. Lacking a detailed study, it may well be that the first "modern" cormorants were small species from eastern, south-eastern or southern Asia, possibly living in freshwater habitat, that dispersed due to tectonic events. Such a scenario would account for the present-day distribution of cormorants and shags and is not contradicted by the fossil record; as remarked above, a thorough review of the problem is not yet available.

Even when Phalacrocorax was used to unite all living species, two distinct genera of prehistoric cormorants became widely accepted today:

The proposed genus Oligocorax appears to be paraphyletic – the European species have been separated in Nectornis, and the North American ones placed in the expanded Phalacrocorax; the latter might just as well be included in Nannopterum. A Late Oligocene fossil cormorant foot from Enspel, Germany, sometimes placed in Oligocorax, would then be referable to Nectornis if it proves not to be too distinct. Limicorallus, meanwhile, was initially believed to be a rail or a dabbling duck by some. There are also undescribed remains of apparent cormorants from the Quercy Phosphorites of Quercy (France), dating to some time between the Late Eocene and the mid- Oligocene. All these early European species might belong to the basal group of "microcormorants", as they conform with them in size and seem to have inhabited the same habitat: subtropical coastal or inland waters. While this need not be more than convergence, the phylogeny of the modern (sub)genus Microcarbo – namely, whether the Western Eurasian M. pygmaeus is a basal or highly derived member of its clade – is still not well understood at all as of 2022.

Some other Paleogene remains are sometimes assigned to the Phalacrocoracidae, but these birds seem rather intermediate between cormorants and darters (and lack clear autapomorphies of either). Thus, they may be quite basal members of the Palacrocoracoidea. The taxa in question are:

The supposed Late Pliocene/Early Pleistocene " Valenticarbo " is a nomen dubium and given its recent age probably not a separate genus.

The remaining fossil species are not usually placed in a modern phylogenetic framework. While the numerous western US species are most likely prehistoric representatives of the coastal Urile or inland Nannopterum, the European fossils pose much more of a problem due to the singular common shag being intermediate in size between the other two European cormorant lineages, and as of 2022 still of mysterious ancestry; notably, a presumably lost collection of Late Miocene fossils from the Odesa region may have contained remains of all three (sub)genera inhabiting Europe today. Similarly, the Plio-Pleistocene fossils from Florida have been allied with Nannopterum and even Urile, but may conceivably be Phalacrocorax; they are in serious need of revision since it is not even clear how many species are involved. Provisionally, the fossil species are thus all placed in Phalacrocorax here:

The former "Phalacrocorax" (or "Oligocorax") mediterraneus is now considered to belong to the bathornithid Paracrax antiqua. "P." subvolans was actually a darter (Anhinga).