He took an interest in the local zoology and spent considerable time outdoors in his early years in India. He was in correspondence with Charles Darwin and at his request he sent him skins of various domestic birds from India and Burma in 1856. He also collaborated with naturalists in India like Thomas C. Jerdon. He collected specimens of molluscs, beached whales and dolphins and a range of other species which were examined by experts in Britain like Richard Owen. He catalogued the mammals of southern India in the "Madras Journal of Literature and Science" and described several new species of small mammals. The rat species "Golunda ellioti" and the Madras tree-shrew "Anathana ellioti" are named after him. W. T. Blanford wrote to him "ery little work is now done on mammals in India. Everybody has gone into ornithology. So far as I am aware your paper in the Madras journal is the only good account ..." Two species of Indian reptiles are named after him: "Monilesaurus ellioti" and "Uropeltis ellioti".