Having earned a large fortune in Sacramento real estate, Harkness retired from his medical practice in 1869, devoting the remainder of his life to the study of natural sciences, especially mycology. Harkness relocated to
San Francisco and was elected a member of the
California Academy of Sciences in 1871, becoming vice president in 1878 and its president from 1887 to 1896. He devoted himself to research into the natural history of the Pacific States, publishing articles on the age of the
Lassen Cinder Cone and the nature of the
fossil footprints discovered near
Carson City, Nevada. He also travelled internationally, visiting North Africa, Europe and the eastern USA several times. Harkness collected, exchanged or purchased over 10,000 specimens of fungi, including many
type specimens, that were donated to the California Academy of Sciences in 1891. Many of these collections were destroyed during the
1906 San Francisco earthquake and fire, though some 480 of his type collections were rescued due to the personal intervention of
Alice Eastwood. These collections were later transferred to the
U.S. National Fungus Collections in
Beltsville, Maryland when California Academy of Sciences herbarium divested itself of its fungal collections late in the 20th century. ==Legacy==