Merkis is a product of Apollon Limassol academies, making his first team debut during 2001-2002 season at the age of 17. After fifteen years at the club, his contract was mutually terminated on 12 January 2016. APOEL
On 12 January 2016, Merkis signed an 18-month contract with fellow Cypriot First Division club APOEL.
He scored his first goal on 16 November 2014, netting the opening goal in Cyprus" 5–0 home victory against Andorra for the Union of European Football Associations Euro 2016 qualifiers.
Cypriot First Division: 2005-2006
Cypriot Cup: 2009-2010, 2012-2013
Cypriot Super Cup: 2006.