Boatman leaves Guantánamo Bay in confusion, for South American country (6)
I believe the answer is:
guyana
'for south american country' is the definition.
(country in South America)
'boatman leaves guantanamo bay in confusion' is the wordplay.
'leaves' indicates named letters should be taken away.
'in confusion' is an anagram indicator.
'guantanamo'+'bay'='guantanamobay'
'guantanamobay' with 'boatman' taken away is 'gunaay'.
'gunaay' with letters rearranged gives 'GUYANA'.
(Other definitions for guyana that I've seen before include "Country E. of Venezuela" , "South American country, a British colony until 1966" , "Off the north coast of S. America, the capital is Georgetown" , "Cricket-playing country" , "South American republic" .)