Gray was a friend of the coleopteristHamlet Clark, and in 1856-57 they voyaged on Gray's yacht Miranda to Spain, Algeria, and Brazil. Gray was an accomplished watercolourist, and his landscape paintings illustrate Clark's account of their journeys. 
During his fifty years employed at the British Museum Gray wrote nearly 500 papers, including many descriptions of species new to science. These had been presented to the Museum by collectors from around the world, and included all branches of zoology, although Gray usually left the descriptions of new birds to his younger brother and colleague George.
Gray was also active in malacology, the study of molluscs.
John Edward Gray was buried at St Mary's Church, Lewisham.
Taxa named by him and in his honour
Gray was one of the most prolific taxonomists in the history of zoology. He described more than 300 species and subspecies of reptiles, only surpassed by his successors at the British Museum, George A. Boulenger and Albert Günther and American zoologist Edward D. Cope.
1824 : "A revision of the family Equidae." Zool. J. Lond. 1 : 241-248 pl. 9.
1824 : "On the natural arrangement of the pulmonobranchous Mollusca." Annals of Philosophy, (n.s.) 8 : 107–109.
1824 : "On the arrangement of the Papilionidae." Annals of Philosophy (n.s.) 8: 119-120.
1825 : "A list and description of some species of shells not taken notice of by Lamarck." Annals of Philosophy (n.s.) 9: 407-415.
1825 : "A synopsis of the genera of reptiles and Amphibia, with a description of some new species." Annals of Philosophy (n.s.) 10 : 193-217.
1825 : "An outline of an attempt at the disposition of the Mammalia into tribes and families with a list of the genera apparently appertaining to each tribe." Annals of Philosophy (n.s.) 10 : 337-344.
1825 : "An attempt to divide the Echinida, or sea eggs, into natural families." Annals of Philosophy (n.s.) 10 : 423-431.
1826 : "Vertebrata. Mammalia." (Appendix B in part). p. 412-415 in King, P.P. (ed.) Narrative of a Survey of the Intertropical and Western Coasts of Australia. Performed between the years 1818 and 1822. With an Appendix, containing various subjects relating to hydrography and natural history. London: J. Murray Vol. 2.
1827 : "Synopsis of the species of the class Mammalia." p. 1-391 in Baron Cuvier The Animal Kingdom Arranged in Conformity with its Organization, by the Baron (G) Cuvier, with additional descriptions by Edward Griffith and others. (16 vols: 1827-1835). London: George B. Whittaker Vol. 5.
1828 : "Spicilegia Zoologica, or original figures and short systematic descriptions of new and unfigured animals." Pt 1. London: Treuttel, Würtz & Co.
1829 : "An attempt to improve the natural arrangement of the genera of bat, from actual examination; with some observations on the development of their wings." Phil. Mag. (ns) 6 : 28-36.
1830 : "A synopsis of the species of the class Reptilia." pp 1–110 in Griffith, E. The animal kingdom arranged in conformity with its organisation by the Baron Cuvier. London: Whitaker and Treacher and Co. 9 : 481 + 110 p.
1830-1835 : "Illustrations of Indian zoology; chiefly selected from the collection of Major-General Hardwicke, F.R.S..." 20 parts in 2 volumes. Illus. Indian Zool.
1831 : "Description of twelve new genera of fish, discovered by Gen. Hardwicke, in India, the greater part in the British Museum." Zool. Misc.
1831 : "Descriptions of some new genera and species of bats." pp. 37–38 in Gray, J.E. (ed.) The Zoological Miscellany. To Be Continued Occasionally. Pt 1. London: Treuttel, Würtz & Co.
1832 : "Characters of a new genus of Mammalia, and of a new genus and two new species of lizards, from New Holland." Proc. Zool. Soc. Lond. 1832 : 39-40.
1832 : Illustrations of Indian zoology; chiefly selected from the collection of Major-General Hardwicke, vol. 1. Treuttel, Wurtz, Treuttel Jun. & Richter, London.
1834 : "Characters of a new species of bat (Rhinolophus, Geoffr.) from New Holland." Proc. Zool. Soc. Lond. 1834 : 52-53.
1837 : "Description of some new or little known Mammalia, principally in the British Museum Collection." Mag. Nat. Hist. (ns) 1 : 577-587.
1838 : "A revision of the genera of bats (Vespertilionidae), and the description of some new genera and species." Mag. Zool. Bot. 2 : 483-505.
1839 : "Descriptions of some Mammalia discovered in Cuba by W.S. MacLeay, Esq. With some account of their habits, extracted from Mr. MacLeay's notes." Ann. Nat. Hist. 4 : 1-7 pl. 1.
1840 : "A Synopsis of the Genera and Species of the Class Hypostoma (Asterias, Linnaeus)." Ann. Mag. Nat. Hist., 6: 275.
1840-10-16 : "Shells of molluscous animals." In: Synopsis of the contents of the British Museum, ed. 42: 105-152.
1840-11-04 : "Shells of molluscous animals." In: Synopsis of the contents of the British Museum, ed. 42, 2nd printing: 106-156.
^ abcdefgBeolens, Bo; Watkins, Michael; Grayson, Michael (2011). The Eponym Dictionary of Reptiles. Baltimore: Johns Hopkins University Press. xiii + 296 pp. ISBN978-1-4214-0135-5. ("Gray", pp. 106-107).