He was also a naturalist who had wide-ranging interests, such that he even described a few species of sea slugs (marine gastropod molluscs).

[1] Cheeseman started studying the flora of New Zealand, and in 1872 he published an accurate and comprehensive account of the plant life of the Waitākere Ranges.

[1] Hundreds of bird specimens added to Auckland Museum's collections by Cheeseman were shot by his younger brother, William Joseph, and their labels bear the tag "W.J.C."

The museum could not afford a taxidermist, but Cheeseman's sister Emma learnt the skill and prepared many of the specimens.

[4] His two other sisters, Ellen, a watercolour painter and botanist, and Clara, a novelist, also accompanied him on field trips.

[5] Cheeseman married Rosetta Keesing, of a notable Jewish family of Auckland city, in November 1889.

In 1906 he produced the Manual of the New Zealand Flora, illustrated by his sister Clara Cheeseman.

[1] As well as his botanical research, Cheeseman developed the Auckland Museum, including what is probably the most extensive collection extant illustrating Māori ethnology.

[3] In 1918, he was awarded the Hector Memorial Medal and Prize, and in 1919 he was made an original Fellow of the New Zealand Institute (FNZInst.).