The type specimen (GMNH-PV-678) of Annakacygna is a nearly complete, almost articulate skeleton discovered in the year 2000 by Hajime Nakajima close to the Usui river, Annaka, Gunma.

[1] The skull of the holotype is crushed and missing most of the rostrum, however based on the preserved mandible a length of 10 cm (3.9 in) has been estimated for the upper beak.

A bony shelf extends over the posterior parts of the orbits, which meets the postorbital process and forms a dorsal notch thought to represent a salt gland.

The musculature of the lower jaw, specifically the adductor mandibulae externus profundus, leaves a wide and deep impression in the bone indicating its origin.

The sternum is poorly preserved, but shows only weak attachment for the coracobrachialis muscle and the coracoid resembles that of the flightless sea duck Chendytes from Pleistocene North America.

The scapula is much stronger than those of extant flying anseriformes with a better developed scapulohumeralis caudalis muscle and initially does not resemble that of a flightless animal.

Both humerus are preserved and are similar in length to those of Black swans, but with an unusually straight shaft lacking a pronounced sigmoid curve.

The radiale is proportionally large while the carpometacarpus is reduced in length, but retaining strong articular surfaces that indicate that the element was still used.

The tarsometatarsus is narrow with an eliptical crosssection, an adaptation observed in grebes and loons that helps reduce drag while moving through water.

This bone is 1.3 times larger than the corresponding material in A. haijimei, which lead the authors to believe that it should represent a species distinct from the type.

[1] Although the upper beak is not preserved, based on the anatomy of the mandible it was likely long and deep with a forward spreading form superficialy resembling modern shovelers.

[1] Due to this combination of skeletal elements and the corresponding musculature, Matsuoka and Hasegawa propose that Annakocygna used its highly specialised wings as a cradle for its young in a fashion similar to extant mute swans.

[1] The feet of Annakacygna are similar in morphology to that of modern diving birds like loons and grebes, showing the same narrowing of the tarsometatarsus, but lacking the shortening of the femur.

Other animals found in the formation include the desmostylian Paleoparadoxia, sharks, allodesmine seals and a variety of cetaceans like Joumocetus, Kentriodon and Norisdelphis.