Bonaparte was raised in Italy and travelled to the United States in 1820 shortly after marrying his cousin Zenaida. Before leaving Italy he had already discovered a warbler new to science, the Moustached Warbler, and on the voyage he collected specimens of a new storm-petrel. On arrival in the United States he presented a paper on this new bird, which was later named after Alexander Wilson.
Bonaparte then set about updating Wilson's American Ornithology, and the revised edition was published between 1825 and 1833. In 1824 Bonaparte tried to get the then unknown John James Audubon accepted by the Academy of Natural Sciences, but this was opposed by the ornithologist George Ord.
After 1828 Charles Bonaparte returned to Italy. He was exiled in 1849 for his involvement in the pro-nationalist movement, and died in Paris.