James Graham Cooper (June 19, 1830 - July 19, 1902) was an American surgeon and naturalist.

Cooper worked for the California Geological Survey (1860-1874) with Josiah Dwight Whitney, Thomas Mayo Brewer and Henry Nicholson Bolander . He was primarily a zoologist, but he also made significant botanical collections from San Diego to Fort Mohave, Arizona in 1861. Cooper was active in the California Academy of Sciences, eventually becoming Director of the Museum.

His father William Cooper was also a naturalist.