His departure follows Sun's decision to offer Java as open source.
James Gosling, inventor of the Java language and also a Sun vice president, will take on Hamilton's responsibilities, Sun said.
Sun would not say why Hamilton left.
"Sun thanks Graham for his many contributions to the company and to Java technology. Graham is widely respected by Sun employees and developers around the world. While it is always sad to see an employee of his caliber depart, we wish him well in all his future endeavors," the company said.
Hamilton recently took a stance against offering Java under the GPL open-source license, questioning Sun's ability to maintain the compatibility of the language.
Hamilton joined Sun in 1995, and participated actively in the development of technologies around Java, such as support for Corba, Java Beans and the JDBC API. He is also known for originating the Java Community Process, and directed Sun's work on Java Standard Edition.
The primary role of the JCP is to coordinate the evolution of the Java language, and to maintain its cohesion and compatibility, especially through certification. It's a role made more difficult by the move to open Java's source code