I have to work with 2 databases.
How can I do it with Hibernate?

Thanks in advance.

Create a DAO factory for each of your databases, each one will use it's own hibernate.properties file and have it's own session factory.

Then use the appropriate DAO factory to execute the queires, get objects etc...

As towny said, use 2 SessionFactoy with different parameters : use hibernate.cfg.xml type configuration, not hibernate.properties for that

how should I set the session factoy parametres as different conf files?

I did:
Configuration conf = new Configuration();
Properties prop = new Properties();
prop.load(new FileInputStream(" ../...../hibernate.myDB1.cfg.xml"));
conf.setProperties(prop);
.... = conf.configure().buildSessionFactory();

but it doesnt work, what am I missing?

very much thanks Emmanuel