Märkl was born on February 11, 1959, in Munich. His father was a violinist, and his mother was a pianist. He took to music at an early age, studying both violin and piano. In 1978, he enrolled at the Hannover Musikhochschule, where he studied violin and piano, as well as conducting with Sergiu Celibidache. He then went on to study conducting with Gustav Meier at the University of Michigan. His first big break came in 1986 when he won the Deutsche Musikrat conducting competition. In 1987, he won a scholarship from the Boston Symphony Orchestra to Tanglewood, where he studied with Leonard Bernstein and Seiji Ozawa. Following several appearances in European opera houses, Märkl received his first music director appointment in 1991 with the Saarbrücken Staatstheater. After leaving Saarbrücken in 1994, he became the music director at Mannheim Nationaltheater, where he worked until 2000. Märkl made his Royal Opera House debut in 1996 with Wagner's Götterdämmerung, and in 1998, he made his Metropolitan Opera debut with Verdi's Il Trovatore. During this time, Märkl also became a regular guest at opera houses in Vienna, Berlin, Munich, and Dresden. He has conducted Wagner's complete Ring Cycle with the Deutsche Oper in Berlin and Tokyo's New National Theatre.
In 2005, Märkl became the music director of the Orchestre National de Lyon, where he went on to record the complete orchestral works of Debussy. He led the Orchestre National de Lyon on tours throughout Europe and to Japan. He remained in this post until 2011. In 2007, while also leading Lyon, Märkl was named the principal conductor of the MDR Symphony Orchestra; he left this position in 2012. He then served as the principal conductor of the Basque National Orchestra from 2014-2017. He was named the principal guest conductor of the Residentie Orchestra in 2018, with the appointment to begin in 2021. He has been a regular guest conductor of major orchestras in Europe, the U.S., Australia, and Japan. These have included the Oslo and Helsinki Philharmonics, orchestras in Boston, Philadelphia, Montreal, Melbourne, and the NHK Symphony. With the NHK Symphony, Märkl recorded the complete symphonies of Robert Schumann.
Märkl has recorded more than 50 albums, primarily for the Naxos label. He has also recorded for MDR and Altus, among others. Besides his surveys of Debussy and Schumann, he also began a survey of Toshio Hosokawa's orchestral music in 2014. In 2019, Märkl released two albums on Naxos: the opera overtures of Albert Lortzing with the Malmö Opera Orchestra and the Saint-Saëns ballet, Ascanio with the Malmö Symphony Orchestra. ~ Keith Finke, Rovi