You can authenticate SSH2 connections with a certificate (public key) just like SSL.
Send the Public key to the SSH2 server administrator.
On the menu bar click Tools > Global Options.
Expand Security.
Click SSH2.
Select the Client's Public/Private key pair check box.
Type the path or browse to your public and private keys in the Public Key Path and Private Key Path boxes.
Select the Use Passphrase check box.
Enter your passphrase in the Use Passphrase and Confirm Passphrase fields.
Click OK.
The public key can only encrypt information. The private key can only decrypt information.
Your private key and passphrase will never be transmitted over a connection. When the server attempts to authenticate:
The server encrypts a random number with your public key and sends it to you.
If you haven't already entered your passphrase in SSH2 security settings, CuteFTP Pro asks you for your passphrase to activate the private key.
The private key decrypts the number and sends it back to the server.
The server recognizes the number as correct and allows the connection.