Instead of making use of the Arima's castles, Matsukura began construction of the new Shimabara Castle and heavily taxed the peasants to pay for it. This oppression of the peasants is what led to the Shimabara Rebellion in the winter of 1637-1638. In an interesting twist of events, the rebels made use of Hara Castle which had simply been abandoned years earlier by Matsukura. The buildings were gone but the moats and walls remained so with little effort the rebels had a fully defensible stronghold.

Shimabara Castle had several different ruling families until the Meiji Period when it was dissassembled.