The otters form the subfamily Lutrinae within the mustelids and the giant otter is the only member of the genus Pteronura.
Two subspecies are currently recognized by the canonical Mammal Species of the World, P. b. brasiliensis and P. b. paraguensis.
Incorrect descriptions of the species have led to multiple synonyms (the latter subspecies is often P. b. paranensis in the literature).
P. b. brasiliensis is distributed across the north of the giant otter range, including the Orinoco, Amazon, and Guianas river systems; to the south, P. b. paraguensis has been suggested in Paraguay, Uruguay, southern Brazil, and northern Argentina, although it may be extinct in the last three of these four.
The World Conservation Union (IUCN) considers the species' presence in Argentina and Uruguay uncertain.
In the former, investigation has shown thinly distributed population remnants.
P. b. paraguensis is supposedly smaller and more gregarious, with different dentition and skull morphology.
Carter and Rosas, however, rejected the subspecific division in 1997, noting the classification had only been validated once, in 1968, and the P. b. paraguensis type specimen was very similar to P. b. brasiliensis.
Biologist Nicole Duplaix calls the division of "doubtful value".

An extinct genus, Satherium, is believed to be ancestral to the present species, having migrated to the New World during the Pliocene or early Pleistocene.
The giant otter shares the South American continent with three of the four members of the New World otter genus Lontra: the neotropical river otter, the southern river otter, and the marine otter. (
The North American river otter (Lontra canadensis) is the fourth Lontra member.)
The giant otter seems to have evolved independently of Lontra in South America, despite the overlap.
The smooth-coated otter (Lutrogale perspicillata) of Asia may be its closest extant relative; similar behaviour, vocalizations, and skull morphology have been noted.
Both species also show strong pair bonding and paternal engagement in rearing cubs.
Giant otter fossil remains have been recovered from a cave in the Brazilian Mato Grosso.

Phylogenetic analysis by Koepfli and Wayne in 1998 found the giant otter has the highest divergence sequences within the otter subfamily, forming a distinct clade that split away 10 to 14 million years ago.
They noted that the species may be the basal divergence among the otters or fall outside of them altogether, having split even before other mustelids, such as the ermine, polecat, and mink.
Later gene sequencing research on the mustelids, from 2005, places the divergence of the giant otter somewhat later, between five and 11 million years ago; the corresponding phylogenetic tree locates the Lontra divergence first among otter genera, and Pteronura second, although divergence ranges overlap.
The otters form the subfamily Lutrinae within the mustelids and the giant otter is the only member of the genus Pteronura. Two subspecies are currently recognized by the canonical Mammal Species of the World, P. b. brasiliensis and P. b. paraguensis. Incorrect descriptions of the species have led to multiple synonyms (the latter subspecies is often P. b. paranensis in the literature). P. b. brasiliensis is distributed across the north of the giant otter range, including the Orinoco, Amazon, and Guianas river systems; to the south, P. b. paraguensis has been suggested in Paraguay, Uruguay, southern Brazil, and northern Argentina, although it may be extinct in the last three of these four. The World Conservation Union (IUCN) considers the species' presence in Argentina and Uruguay uncertain. In the former, investigation has shown thinly distributed population remnants. P. b. paraguensis is supposedly smaller and more gregarious, with different dentition and skull morphology. Carter and Rosas, however, rejected the subspecific division in 1997, noting the classification had only been validated once, in 1968, and the P. b. paraguensis type specimen was very similar to P. b. brasiliensis. Biologist Nicole Duplaix calls the division of "doubtful value".
An extinct genus, Satherium, is believed to be ancestral to the present species, having migrated to the New World during the Pliocene or early Pleistocene. The giant otter shares the South American continent with three of the four members of the New World otter genus Lontra: the neotropical river otter, the southern river otter, and the marine otter. (The North American river otter (Lontra canadensis) is the fourth Lontra member.) The giant otter seems to have evolved independently of Lontra in South America, despite the overlap. The smooth-coated otter (Lutrogale perspicillata) of Asia may be its closest extant relative; similar behaviour, vocalizations, and skull morphology have been noted. Both species also show strong pair bonding and paternal engagement in rearing cubs. Giant otter fossil remains have been recovered from a cave in the Brazilian Mato Grosso.
Phylogenetic analysis by Koepfli and Wayne in 1998 found the giant otter has the highest divergence sequences within the otter subfamily, forming a distinct clade that split away 10 to 14 million years ago. They noted that the species may be the basal divergence among the otters or fall outside of them altogether, having split even before other mustelids, such as the ermine, polecat, and mink. Later gene sequencing research on the mustelids, from 2005, places the divergence of the giant otter somewhat later, between five and 11 million years ago; the corresponding phylogenetic tree locates the Lontra divergence first among otter genera, and Pteronura second, although divergence ranges overlap.
Giant otter