PersistenceUnit vs PersistenceContext

EntityManager obtained via @PersistenceContext is called Container Managed EntityManager as container will be responsible for managing "EntityManager". EntityManager obtained via @PersistenceUnit / entityManagerFactory.createEntityManager() is managed in the application by the developer. (for e.g. managing lifecycle of EntityManager, releasing the resources acquired by EntityManager, etc.).

PersistenceUnit injects an EntityManagerFactory, and PersistenceContext injects an EntityManager. It's generally better to use PersistenceContext unless you really need to manage the EntityManager lifecycle manually.

I don't know how it works exactly in the Java EE, but in Spring, when you specify @PersistenceContext annotation, it injects EntityManager. Where does it get EntityManager? It is wrong to create one EntityManager for the whole application lifetime by calling EntityManagerFactory.createEntityManager(). So instead a special implementation of EntityManager interface is used and instantiated directly. It has an internal mutable thread-local reference to a real EntityManager. Implementations of methods just redirect calls to this real EntityManager. And there is a servlet listener, that before each request obtain EM by calling EMF.createEntityManager() and assign it to that inner reference of special EM. Also this listener manages transactions by calling getTransaction().begin(), .commit() and .rollback() on the real EM. It is very simplified description of performed work. And I believe, that JEE container does the same thing, as Spring does.

In general case it is better to inject EntityManager, because with EntityManagerFactory and @PersistenceUnit you should create/destroy EntityManager every time by hands and manage transactions too.