The city and province were given up to anarchy; the coloured people, elated with victory, proclaimed the slaughter of all whites, except the English, French, and American residents.

He then moved up the Amazon to Óbidos Manaus and finally to the Upper Amazon (Solimões). He was most famous for his expedition to the rainforests of the Amazon with Alfred Russel Wallace starting in 1848. He spent the next three years writing his account of the trip The Naturalist on the River Amazons widely regarded as one of the finest reports of natural history travels.

When Bates arrived home in 1859 after a full eleven years he had sent back over 14712 species (mostly of insects) of which 8000 were new to science. Bates wrote up his findings in his best-known work The Naturalist on the River Amazons. He was most famous for his expedition to the rainforests of the Amazon with Alfred Russel Wallace starting in 1848.