Can someone please explain to me the difference in the EAR versions.
Is it tied to the JDK version 1.4, 5 and 6?
Thanks.

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It is not JDK version. It is J2EE/Java EE version.
It is asking you which J2EE/Java EE version the ear format (deployment descriptor etc) should adhere to: J2EE 1.2 or 1.3 or 1.4 or Java EE 5 or Java EE 6.
Application servers publish their compliance levels. And some application servers generally support older ear versions as well. For e.g. WebSphere 6.x is J2EE 1.4 compliant but it can still run 1.3 ear version.