After that, the islands became a base for pirates and a target for Dutch merchants intent on opening up trade with China. The Dutch captured the Pescadores in 1622 and built a fort there.
明太祖時曾廢澎湖巡檢司，毀棄建設，並遷徙人民到福建漳州、泉州，澎湖遂成為海盜倭寇的巢穴、荷蘭人覬覦的目標。