Markus Fothen (born 9 September 1981 in Kaarst) is a retired German road racing cyclist, who rode as a professional between 2004 and 2013.

In 2003 Fothen won the under-23 World Championship time trial in Hamilton, Canada. He completed the 30.8 km course in 38:35.29, beating his nearest rival by nearly 20 seconds.

During 2006 Tour de France, Fothen held the white jersey as leader of the young rider classification for 13 stages, losing it to Damiano Cunego on the 17th stage. He finished the Tour 38 seconds behind Cunego.