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Both annotations originate from different APIs, and have been specified (more or less) independently. While the JSF session annotation has a clear focus on the JSF view technology, CDI requires a session annotation which is present, no matter if JSF is deployed or not (CDI can be used without JSF). So CDI had no choice but defining it's own session scope. Unfortunately, Java EE 6 did not align this very well.

You should always use scopes from javax.enterprise.context when using CDI