Thomas was born on June 27, 1874, in Cincinnati, Ohio. He graduated from Knoxville High School and entered the University of Tennessee in 1889 at the age of 15! He assisted agrostologist F. Lamson-Scribner at the University in 1892, and did a special course in botany and geology at Columbia as assistant curator under N. L. Britton in 1893. Thomas was assistant agrostologist from 1894 to 1897 in Washington under Lamson-Scribner. He transferred to assistant botanist under Fred Coville and conducted botanical surveys of the Dismal Swamp of Virginia in 1898 and participated in the Harriman Alaska Expedition from 1898 to 1900. From 1900 to 1944, he was physiologist, rising through ranks in the Bureau of Plant Industry, spending time in the Southwest studying growth on alkali soils in 1901.
From 1902 to 1905, he traveled in North Africa, Tunisia, and Sicily studying crops like dates and pistachios, which were introduced into the southwest. He also studied cotton in Egypt and began work in Arizona breeding cotton, including long-staples like Pima cotton. In 1920, the University of Arizona gave him an honorary LLD degree in recognition of his work with Pima cotton. He expanded from cotton to become the world expert on the Malvaceae. From 1925 to 1940, he became interested in the flowering plants and ferns of Arizona, upon which he published in 1942 with Peebles. He retired in 1944 at the age of 70 and moved to San Francisco to work, at the invitation of Alice Eastwood, as research associate in botany at the California Academy of Sciences, revising the Arizona flora in 1951. On August 28, 1956, he was awarded a Certificate of Merit by the Botanical Society of America “for early theoretical contributions to plant geography, his work in cotton breeding, his systematic studies in Malvaceae, and his part in the preparation of the Flora of Arizona.”
Thomas was a founding member and on the organizing committee of the Washington Biologists’ Field Club in 1900, but was terminated for not paying founding dues. He was elected in 1902 and was awarded an honorary membership in 1944. He died on October 19, 1956, in San Francisco, California.