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Eventually, it was recognized that bowheads and right whales were in fact different, but there was still no strong consensus as to whether they shared a single genus or two. Studies in the 2000s finally provided clear evidence that the three living right whale species do comprise a phylogenetic lineage, distinct from the bowhead, and that the bowhead and the right whales are rightly classified into two separate genera.

As recently as 1998, Dale Rice, in his comprehensive and otherwise authoritative classification, Marine mammals of the world: systematics and distribution, listed just two species: B. Balaena prisca, one of the five Balaena fossils from the late Miocene (~10 Mya) to early Pleistocene (~1.5 Mya), may be the same as the modern bowhead whale.

Seemingly identical to its cousins in the North Atlantic, North Pacific and Southern Oceans, they were all thought to be a single species, collectively known as the "right whale", and given the binomial name Balaena mysticetus.

Today, the bowhead whale occupies a monotypic genus, separate from the right whales, as was proposed by the work of John Edward Gray in 1821.

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