Unexpected gem in a puzzle (6)
I believe the answer is:
enigma
'puzzle' is the definition.
(thesaurus)
'unexpected gem in a' is the wordplay.
'unexpected' indicates an anagram.
'gem'+'in'='gemin'
'gemin' anagrammed gives 'enigm'.
'enigm'+'a'='ENIGMA'
(Other definitions for enigma that I've seen before include "'Mystery, riddle (6)'" , "Riddle - German coding machine" , "German military cipher machine" , "Puzzle for gaming" , "Difficult problem" .)