In addition to collecting, Ayres catalogued and sketched the plants in the wild, as was common among nineteenth century naturalists.
He also planned to write a book about the flora of Mauritius, but he died from relapsing fever in his home in Port Louis on 30 April 1863 before the flora could be accomplished.
Ayres' wife Harriet collected his written records and bequeathed them to the Royal Botanic Gardens, Kew.
His eldest son Philip Burnard Chenery Ayres (1840–1899) became a well-known surgeon in Hong Kong.