Molecular studies have been made on dugong populations using mitochondrial DNA. The results have suggested that the population of Southeast Asia is distinct from the others. Australia has two distinct maternal lineages, one of which also contains the dugongs from Africa and Arabia. Limited genetic mixing has taken place between those in Southeast Asia and those in Australia, mostly around Timor. One of the lineages stretches all the way from Moreton Bay to Western Australia, while the other only stretches from Moreton Bay to the Northern Territory. There is not yet sufficient genetic data to make clear boundaries between distinct groups.
The dugong's body is large with a cylindrical shape that tapers at both ends. It has thick, smooth skin that is a pale cream colour at birth, but darkens dorsally and laterally to brownish-to-dark-grey with age. The colour of a dugong can change due to the growth of algae on the skin. The body is sparsely covered in short hair, a common feature among sirenians which may allow for tactile interpretation of their environment. These hairs are most developed around the mouth, which has a large horseshoe-shaped upper lip forming a highly mobile muzzle.This muscular upper lip aids the dugong in foraging. Bones in the forelimb can fuse variously with age.
The dugong's tail flukes and flippers are similar to those of dolphins. These flukes are raised up and down in long strokes to move the animal forward, and can be twisted to turn. The forelimbs are paddle-like flippers which aid in turning and slowing. The dugong lacks nails on its flippers, which are only 15% of a dugong's body length. The tail has deep notches.
A dugong's brain weighs a maximum of 300 g (11 oz), about 0.1% of the animal's body weight. With very small eyes, dugongs have limited vision, but acute hearing within narrow sound thresholds. Their ears, which lack pinnae, are located on the sides of their head. The nostrils are located on top of the head and can be closed using valves. Dugongs have two teats, one located behind each flipper. There are few differences between sexes; the body structures are almost the same. A male's testes are not externally located, and the main difference between males and females is the location of the genital aperture in relation to the umbilicus and the anus. The lungs in a dugong are very long, extending almost as far as the kidneys, which are also highly elongated in order to cope with the saltwater environment. If the dugong is wounded, its blood will clot rapidly.
The skull of a dugong is unique. The skull is enlarged with sharply down-turned premaxilla, which are stronger in males. The spine has between 57 and 60 vertebrae. Unlike in manatees, the dugong's teeth do not continually grow back via horizontal tooth replacement. The dugong has two incisors (tusks) which emerge in males during puberty. The female's tusks continue to grow without emerging during puberty, sometimes erupting later in life after reaching the base of the premaxilla. The number of growth layer groups in a tusk indicates the age of a dugong, and the cheekteeth move forward with age. The full dental formula of dugongs is 2.0.3.33.1.3.3, meaning they have two incisors, three premolars, and three molars on each side of their upper jaw, and three incisors, one canine, three premolars, and three molars on each side of their lower jaw. Like other sirenians, the dugong experiences pachyostosis, a condition in which the ribs and other long bones are unusually solid and contain little or no marrow. These heavy bones, which are among the densest in the animal kingdom, may act as a ballast to help keep sirenians suspended slightly below the water's surface.