Born in Weimar, Werner studied painting under Julius Schnorr von Carolsfeld in Leipzig. He switched to studying architecture in Munich from 1829 to 1831, but thereafter returned to painting. He won a scholarship to travel to Italy, where he ended up founding a studio in Venice and remaining until the 1850s, making a name for himself as a watercolor painter. He exhibited around Europe, in particular traveling often to England, where he exhibited at the New Watercolour Society.
He traveled through Spain in 1856 and 1857, and then in Egypt and Palestine from 1862 to 1864. Particularly notable were his watercolors in Jerusalem, where he was one of the few non-Muslims able to gain access to paint the interior of the Dome of the Rock. He published some watercolors from this trip in 1875 as Carl Werner's Nile Sketches. He later traveled to Greece and Sicily, and became a professor at the Leipzig Academy, dying in Leipzig in 1894.
His works include:
- “Venice in her Zenith and Decline”
- “The Ducal Palace, with a Scene from the Merchant of Venice”
- “The Triumphal Procession of Doge Cantarini” (5 ft. high),
- “The Zisa Hall in Palermo”
- “The Lions' Court of the Alhambra”
- Jerusalem and the Holy Land, comprises 30 designs, published with text and colored plates (London, 1866-7)
- Lynne Thornton (1994). "Carl Werner". The Orientalists: Painter-Travellers. ACR Edition. p. 182. ISBN 2-86770-083-3.
- "Werner, Karl". The American Cyclopædia. 1879.
- Hermann Arthur Lier (1897), "Werner, Karl Friedrich Heinrich", Allgemeine Deutsche Biographie (ADB) (in German) 42, Leipzig: Duncker & Humblot, pp. 61–63
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