In linguistics, marked has (at least) two different, near-contradictory meanings:
Marked as containing a marker: The plural is marked by
'-s'. This form of 'marked' means that a feature is somehow present in the speech. 'Unmarked' in this sense means a sort of default form: the singular is unmarked.
Marked as being remarkable: OVS word order is highly marked. This form of 'marked' means that its appearance is an unusual occurrence. 'Unmarked' in this sense is also a sort of default form; "I like cheese" has unmarked word order in English.