Y
- (Aso-gun) Yamatsuno
- (Aso-gun) Yumita
- (Aso-gun) Yanase
- (Aso-gun) Yamagawa
- (Aso-gun) Yumoto
- (Aso-gun) Yuyama
- (Kamimashiki-gun) Yonaigura
- (Amakusa Shi) Yoshida
- (Amakusa Shi) Yamanotori
- (Amakusa Shi) Yairagi
- (Amakusa Shi) Yamanoura
- (Amakusa Shi) Yamaguchi
- (Amakusa Shi) Yamago
- (Amakusa Shi) Yamanokuchi
- (Amakusa Shi) Yokohama
- (Amakusa Shi) Yamanaka
- (Amakusa Shi) Yokoshima
- (Amakusa Shi) Yokono
- (Amakusa Shi) Yakata
- (Amakusa Shi) Yokokubo
- (Amakusa Shi) Yamanoguchi
- (Amakusa Shi) Yamanote
- (Amakusa Shi) Yokogashira
- (Amakusa Shi) Yunuki
- (Amakusa Shi) Yanagida
- (Amakusa Shi) Yufunehara-shimo
- (Amakusa Shi) Yufunehara-kami
- (Amakusa Shi) Yokomichi
- (Amakusa Shi) Yamasaki
- (Amakusa Shi) Yamaura