I am using Hibernate with EntityManager.

For some reason, unless I define my entity class in both persistence.xml and hibernate.cfg.xml, I get a "xxx is not mapped" exception. If I define it in both, I am fine.

Is there any way around this?

I think you should delete one of them, you either use JPA and configure it by using persistence.xml or plain hibernate and use the other configuration file.
Even when using JPA you should be able to set most hibernate options in the persistence.xml.

Or you could include the hibernate configuration in the persistence one using the

But you certainly don't have to declare the entities in both.

Sanne