The Mail app allows the use of S/MIME certificates for encryption/decryption.
It's also possible to use PGP or GPG in one of their incarnations, for example https://gpgtools.org.
Effectively, the encrypted message (and any attachments) becomes a file attachment to a regular but otherwise empty mail between two peers.
Note that two-way encrypted communications require that your communication peers are capable of encrypting and decrypting messages too.