As a teenager, the 6 ft 5 in tall Rogan swam for Mount Vernon High School (Alexandria, Virginia) in Fairfax County, Virginia, where he trained with the Curl-Burke Swim Club. In July 2000, he cut short his final season of the Northern Virginia Swim League, swimming for the Mansion House Piranhas (of Mount Vernon), and flew to Australia where he competed in the 2000 Sydney Olympics, failing to advance beyond the heats in the backstroke. He earned a scholarship to attend Stanford University from 2000-2004. On 8 December 2005, in Trieste, Markus set a new world record in the 200 m backstroke for short course swim pools, with 1:50.43. This world record was then broken by American swimmer Ryan Lochte, who lowered the standard to 1:49.05 at the 2006 FINA Short Course World Championships in Shanghai, China. Back on the short course in Manchester 2008, Rogan broke the world record again on 13 April 2008, setting the new record with 1:47.84, with Lochte finishing second by seven one-hundredths of a second (also under the old world record). Both swimmers were wearing the new Speedo LZR Racer swimsuit.
In an interview with BBC Sport at the 2008 European Championships in Eindoven, The Netherlands, in March 2008, Markus told reporters that he was planning to retire from competitive swimming after the Beijing Olympics in August. Markus won both the 100 and 200 metre backstroke events (long course) at those European Championships.
In the meantime Rogan changed his plans on retirement. He swam at the World Championships 2009 in Rome. As he is training in Italy, the event is virtually on homeground and he wants to enjoy the home event with his Italian training partners.