Franz Josef Maria Werner (15 August 1867 in Vienna – 28 February 1939 in Vienna) was an Austrian zoologist and explorer. Specializing as a herpetologist and entomologist, Werner described numerous species and other taxa of frogs, snakes, insects, and other organisms. Although working close to the Vienna Natural History Museum, he could not use their herpetological collections, after the death of its director, Franz Steindachner (1834–1919), who did not like Werner, and had barred him from accessing the collections.