Not wanting to link identities is understandable. I keep a few separate identities myself. As for the confusion between keys... Version: GnuPG v1.4.12 (GNU/Linux) I don't know how you use PGP on Linux, but there's little room for confusion with command line gpg, especially in interactive mode. If you decrypt or verify, it selects the key for you. If you encrypt, it prompts you for the keys to use. The only source of confusion is during clear signing. For that... Open ~/.gnupg/gpg.conf and find the line that says default-key. Pick the key you use most often and put the key ID there. When you want to use the other one, use the --default-key argument. gpg --default-key <my secret identity key> --clear-sign