I am using native generator to generate my primary key id for two of my objects. The id mapping of both of my objects look like this (note that the classes are mapped to two different tables):

<id name="id" column="id" type="long">
<generator class="native"/>
</id>

Now the problem is that when I create an object of each class and save it to the DB using the session.save() method. The first objects that is saved gets an id of 1 and the second object gets 2. Shouldn't both get an id of 1 since they are in a different table?

Note that I am using Oracle and that I start with clean tables with no entries.

No, the generator creates a unique id for every object you ever save

The native generator for Oracle is a single sequence so your result is correct. You can define an argument against native generator to select the sequence to use. Have a look at the docs for sequence id generator.