[1] He was eventually chosen by the San Antonio Spurs in the second round of the 2006 NBA draft, 59th overall, then immediately traded to the Milwaukee Bucks.

In February 2007, the Bucks assigned Markota to Tulsa 66ers of the NBA Development League, in order to further improve his play.

[2] On September 7, Markota was waived by the Bucks,[3] and signed with Russian team Spartak St. Petersburg on a two-year contract two days later.

[5] On August 14, 2008, Markota was signed by Cibona, returning to the team he represented as a youngster[6] but, after a series of unsatisfying performances upon recovering form knee injury, he was suspended for clashing with the coach.

[11] In January 2012 he left Union Olimpija due to lack of payment and signed with KK Zagreb.

[23] Markota started the 2020–21 season with the Croatian side Zabok but on October 23, 2020, he signed with Cibona for the fifth time in his career.