Markota, born in Sarajevo (then SR Bosnia and Herzegovina, SFR Yugoslavia), fled Bosnia during the war and settled in Sweden, where he began to practice basketball. He played together with Maciej Lampe in Stockholm, until moving to Croatia when he was fourteen, after being invited to play in the Croatian league. Markota signed with KK Cibona, but was loaned to Zabok and "Karlovac Šanac" until the end of 2002–03. Subsequently, he received Croatian citizenship (holding Swedish as well), declining an offer to play for the Swedish national basketball team.