A number of plant, animal and fungal species have been named to his honour, e.g. Saxifraga nathorstii (Dusén) Hayek (East Greenland saxifrage) and a suite of fossil plant species, Williamsonia nathorstii Carruthers (a fossil dragonfly) and Laestadites nathorstii Mesch. (a fossil fungus).
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It was named by A.G. Nathorst on his 1899 expedition as Konung Oscars Fjord for Oscar II, King of Sweden from 1872–1907.