Leader of Samurai in tree by a Japanese city (5)
I believe the answer is:
osaka
'japanese city' is the definition.
(city in Japan)
'leader of samurai in tree by a' is the wordplay.
'leader of' indicates taking the first letters.
'in' means one lot of letters goes inside another.
'tree' becomes 'oak' (oak is a kind of tree).
'by' is a charade indicator (letters next to each other).
The initial letter of 'samurai' is 's'.
's' placed within 'oak' is 'osak'.
'osak'+'a'='OSAKA'
(Other definitions for osaka that I've seen before include "S. Japan port, bay" , "Third most populous Japanese city" , "Japanese city near Kobe" , "Port city on Honshu, Japan" , "Asian" .)