Imagine you have two implementations of a @Local interface
@Local
public interface LocalInterface {
}
@Stateless
public class MyFirstImplementa
You can achieve it using the deployment descriptor - ejb-jar.xml. Something like this (might not be 100% accurate, but I think you've got the point):
MyClass
ejb/myLocalReferencedBean
Session
com.yourpackage.LocalInterface
MyFirstImplementation
local
MyFirstImplementation
MySecondImplementation
Another way is to use the CDI as described here: Inject @EJB bean based on conditions