His main castle is located in Koopa Kingdom, but has many more spread through out the Mushroom Kingdom. Bowser's castles and fortresses have constantly undergone changes through many different Mario games (Most of the time it ends up being destroyed by the game's events), never appearing the same from other games.
Bowser Keep (Super Mario RPG)Edit
A castle is isolated on a mountain of red, jagged rocks. The Keep rest on the biggest rock that resembles Bowser himself. The keep can only be access by a long bridge that is connect to Faraway Vista Hill. The halls are lined with statues of Hammer Bros. and Bowser. Additionally lava flows through as well that can only be crossed by wooden bridges.
It was mainly guard by Terrapin soldiers until it was taken by the Smithy Gang that used it as their Headquarters while they were in the Mushroom World.
Neon Castle Edit
Located in the Valley of Bowser which beneath Dinosaur Land. Has two doors that let you into the Castle, the main one open right to the Koopa Troopa, while the back door lead to Bowser's personal chamber.
Bowser's Castle (Paper Mario)Edit
In Paper Mario, Bowser uses this castle to kidnap Princess Peach, he put her castle ontop of his.
In Superstar Saga, Bowser's Fortress flies over to the Beanbean Kingdom under the command of Bowletta, who uses it to attack Beanbean Castle Town. Mario and Luigi, with the aid of Prince Peasly, venture through the castle and defeat Bowletta. Peasly destroys the castle with bombs, leaving Bowser inside to blown out by the explosion.