I have WordPress and ZenPhoto installed in the same database. Now I moved my site to another domain (same server) and already installed WP. Now I want to restore the ZP backup, but it will empty the existing tables first. But does this mean all tables in that database? I use a different prefix for WP and ZP.

If you are talking of the Zenphoto backup/restore utility it will delete only the Zenphoto tables (by the prefix you specified)

Yes, I meant the ZP utility. Thanks.