James Yate Johnson (c. 1820, in Kendal, Westmorland – 2 February 1900, in Funchal) was an English naturalist.
Johnson lived in Madeira from around 1851, studied marine fish, crustacea, sea anemones and sponges and terrestrial spiders, flowering plants and mosses.
He collected specimens for other naturalists; for instance, George Busk, who in 1859 wrote "Zoophytology: On some Madeiran Polyzoa."
Johnson explored the São Vicente Caves after being informed of their existence by locals on Madeira in 1885.
[1] He was the son of John Henry Johnson and Ann Yate, also brother of John Henry Johnson (patent attorney).