The Merkensteiners sat in the castle until 1322, until they had to pass it on. The next important castle owners were the Wallseers, who held Merkenstein Castle (also Merchenstein or Marchinstein) for a good 100 years until they had to pass the castle on to Stephan von Hohenberg in 1440 for financial and family reasons. The Hohenberger ruled over Merkenstein until 1484. The castle was once the scene of an imperial siege. In 1482 the then lord of the castle, Hans III. von Hohenberg made his castles Merkenstein, Hohenberg and Kreisbach available to the Hungarian king Matthias Corvinus in his war against Emperor Friedrich III. The emperor then sent an army against Merkenstein, but the siege failed after a total of four weeks. 1484 had Hans III. reconciled with Friedrich and then sold Merkenstein Castle to him. The castle was now sovereign and received by imperial envoys. In 1486, however, King Matthias Corvinus returned and conquered Merkenstein. After his death, the castle reverted to the empire. From 1603 to 1672 it was owned by the Heißperger family, then by the Dietrichsteiner. In August 1683, after a long siege, Ottoman troops succeeded in taking the castle and setting it on fire. 173 people lost their lives in the castle. Since then the castle has fallen into disrepair. The outer walls of quarry stone are still relatively well preserved. Due to the lack of ring walls, they are particularly strong (up to 6 m). After the destruction, the Dietrichsteiner estate administration was moved to the old Gainfarn Castle.
Until the end of the Second World War, the castle and the estate were owned by the German line of the Krupp family. Therefore, after the war (1945-1955) it fell into the USIA administration of the Soviets as German property. According to the state treaty, the castle became the property of the republic and thus of the federal forests. The castle has been privately owned since 1978 and has been carefully restored ever since.
The German composer Ludwig van Beethoven dedicated two songs to the ruins of Merkenstein.
In October 2008, the ruins were the scene of filming for the television crime series Four Women and a Death