His plant collections are housed in the Rancho Santa Ana Botanic Garden, in Claremont, and also in the Gray Herbarium of Harvard University.

In 1925, German botanist August Brand, named a genus of flowering plants (belonging to the family Boraginaceae) from South America and the southern United States, as Johnstonella in Johnston's honour.

[2] Then in 1933, botanist O.E.Schulz named a genus of flowering plants (belonging to the family Brassicaceae), from Chile as Ivania.

[3] In 1936, botanist Hsen Hsu Hu published Sinojohnstonia, which is a genus of flowering plants from China, belonging to the family Boraginaceae.

[4] In 1975, another botanist Syed Muhammad Anwar Kazmi, named a monotypic genus of flowering plants (belonging to the family Boraginaceae), from the Western Himalaya region, Ivanjohnstonia also named in his honour.