The son of a stocking-factory owner in the central English town of Leicester, Bates left school at 13 and was apprenticed to a hosiery manufacturer, but still found time for indulging his hobby of beetle collecting. In 1844 he met Alfred Wallace and stimulated the latter's interest in entomology. This led, three years later, to Wallace suggesting they should travel together to the tropics to collect specimens and data that might throw light on the evolution of species.

In May 1848 they arrived at Pará, Brazil, near the mouth of the Amazon. After two years collecting together they split up, and Bates spent a further nine years in the Amazon basin. By the time he returned to England in 1859, he estimated he had collected 14,712 species, 8000 of which were new to science.

While collecting Bates had noted startling similarities between certain butterfly species – a phenomenon later to be termed Batesian mimicry. He attributed this to natural selection, since palatable butterflies that closely resembled noxious species would be left alone by predators and thus tend to increase. His paper on this, Contributions to an Insect Fauna of the Amazon Valley, Lepidoptera: Heliconidae (1861) provided strong supportive evidence for the Darwin– Wallace evolutionary theory published three years earlier.

Darwin persuaded Bates to write a book on his travels, which resulted in the appearance of The Naturalist on the River Amazon (1863), an objective account of the animals, humans, and natural phenomena Bates encountered. Although one of the best and most popular books of its kind, Bates was to comment that he would rather spend a further 11 years on the Amazon than write another book. He became assistant secretary of the Royal Geographic Society in 1864.