1913

• Anthony, H.E. 1913. Mammals of northern Malheur County, Oregon. Bulletin of the American Museum of Natural History 32: 1–27 + 2 plates.

1914

• Anthony, H.E. 1914. A new rabbit and a new bat from neotropical regions. Bulletin of the American Museum of Natural History 37: 335–337 + 1 plate.

1916

• Anthony, H.E. 1916a. Habits of Aplodontia. Bulletin of the American Museum of Natural History 35: 53–59 + 4 plates.
• Anthony, H.E. 1916b. Panama mammals collected in 1914–1915. Bulletin of the American Museum of Natural History 35: 357–375.
• Anthony, H.E. 1916c. Preliminary diagnosis of an apparently new family of insectivores. Bulletin of the American Museum of Natural History 35: 725–728 + 1 plate. 

1917

• Anthony, H.E. 1917a. New fossil rodents from Porto Rico ; with additional notes on Elasmodontomys obliquus Anthony and Heteropsomys insulans Anthony. Bulletin of the American Museum of Natural History 37: 183–189 + 1 plate. 
• Anthony, H.E. 1917b. Two new fossil bats from Porto Rico. Bulletin of the American Museum of Natural History 37: 565–568 + 1 plate.

1918

• Anthony, H.E. 1918. The indigenous land mammals of Porto Rico, living and extinct. Memoirs of the AMNH 2(2): 334–435 + 20 plates.

1919

• Anthony, H.E. 1919. Mammals collected in eastern Cuba in 1917 : with descriptions of two new species. Bulletin of the American Museum of Natural History 41: 625–643 + 3 plates.

1920

• Anthony, H.E. 1920a. New rodents and new bats from neotropical regions. Journal of Mammalogy 1: 81–86.
• Anthony, H.E. 1920b. New mammals from Jamaica. Bulletin of the American Museum of Natural History 42: 469–475 + 2 plates.

1921

• Anthony, H.E. 1921a. New mammals from British Guiana and Colombia. American Museum Novitates 19: 1–7.
• Anthony, H.E. 1921b. Preliminary report on Ecuadorean mammals. No. 1. American Museum Novitates 20: 1–6.
• Anthony, H.E. 1921c. Mammals collected by William Beebe at the British Guiana Tropical Research Station. Zoologica 3: 265–285.

1922

• Anthony, H.E. 1922a. Preliminary report on Ecuadorean mammals. No. 2. American Museum Novitates 32: 1–7.
• Anthony, H.E. 1922b. A new fossil rodent from Ecuador. American Museum Novitates 35: 1–4.

1923

• Anthony, H.E. 1923a. Mammals from Mexico and South America. American Museum Novitates 54: 1–10.
• Anthony, H.E. 1923b. Preliminary report on Ecuadorean mammals. No. 3. American Museum Novitates 55: 1–14. Full article Reference page. 

1924

• Anthony, H.E. 1924a. A new fossil perissodactyl from Peru. American Museum Novitates 111: 1–3.
• Anthony, H.E. & Goodwin, G.G. 1924 A new species of shrew from the Gaspé Peninsula. American Museum Novitates 109: 1–2.
• Anthony, H.E. 1924b. Preliminary report on Ecuadorean mammals. No. 4. American Museum Novitates 114: 1–6. Full article Reference page. 
• Anthony, H.E. 1924c. Preliminary report on Ecuadorean mammals. No. 5. American Museum Novitates 120: 1–3. Full article Reference page. 
• Anthony, H.E. 1924d. Preliminary report on Ecuadorean mammals. No. 6. American Museum Novitates 139: 1–9. Full article Reference page. 

1925

• Anthony, H.E. 1925. New species and subspecies of Thomasomys. American Museum Novitates 178: 1–4. Full article Reference page. 

1926

• Anthony, H.E. 1926a. Two new rodents from Bolivia. American Museum Novitates 178: 1–4. Full article Reference page. 
• Anthony, H.E. 1926b. Preliminary report on Ecuadorean mammals. No. 7. American Museum Novitates 240: 1–6. Full article Reference page. 

1929

• Anthony, H.E. 1929. Two new genera of rodents from South America. American Museum Novitates 383: 1–6.

1932

• Anthony, H.E. 1932a. A new species of Thomasomys from Venezuela. American Museum Novitates 548: 1–2.
• Anthony, H.E. 1932b. A new genus of rodents from Yucatán. American Museum Novitates 586: 1–3.

1935

• Anthony, H.E. & Tate, G.H.H. 1935. Notes on South American Mammalia. No. 1. Sciurillus. American Museum Novitates 780: 1–13.

Eponyms

(List may be incomplete)

• 1 eponyms of Harold Elmer Anthony
• Phyllobates anthonyi Noble, 1921 [accepted as Epipedobates anthonyi]
• Hypsugo anthonyi Tate, 1942
• †Gallinago anthonyi Wetmore, 1920 [accepeted as Scolopax anthonyi]
• Felis concolor anthonyi Nelson & Goldman, 1931 [accepeted as Puma concolor anthonyi]
• †Stenoderma rufum anthonyi Choate & Birney, 19688
• †Artibeus anthonyi Woloszyn & Silva, 1977