Specializing as a herpetologist and entomologist, Werner described numerous species and other taxa of frogs, snakes, insects, and other organisms.

A brilliant student, he corresponded often with George Albert Boulenger (1858–1937) and Oskar Boettger (1844–1910) who encouraged his studies with these animals.

Werner succeeded in constituting an immense personal collection, and published more than 550 publications principally on herpetology.

He named many new species of reptiles, amphibians, and arthropods, of which he specialized in orthopterans and scorpions.

His book, Amphibien und Reptilien (1910), contributed to the popularization of terraphilia, or raising pet reptiles and amphibians in terraria.