After that, Yodo kojo Castle was successively governed by Hikan of the Hosokawa family, but control was gradually transferred from the Hosokawa's government (Sengoku Period (Period of Warring States)) to Miyoshi's government and when Nagayoshi MIYOSHI unified Kyoto in 1559, Ujitsuna HOSOKAWA became the Joshu (castellan) of Yodo kojo Castle, and upon the death of Ujitsuna HOSOKAWA in 1563, Yoshitsugu MIYOSHI succeeded him, and subsequently a Busho (Japanese military commander) belonging to Hisahide MATSUNAGA appeared to govern the castle.
その後細川氏の被官が代々淀古城を治めていたが、細川政権(戦国時代)から三好政権に移っていき、1559(永禄2年）には三好長慶が京を統一すると淀古城も細川氏綱が城主となったが、1563(永禄6年）にその細川氏綱も死去すると、三好義継が城主となり、ついで松永久秀方の武将が城主となったようである。