You should get an SSH host key fingerprint along with your credentials from a server administrator. Knowing the host key fingerprint and thus being able to verify it is an integral part of securing an SSH connection. It prevents man-in-the-middle attacks.
In the real world, most administrators do not provide the host key fingerprint.
Instead you can ask anyone else with a physical access to the server. The host key is only one and hence the same for all users. Also note that the host key fingerprint is generated from a public key part of the host key only. So it is not secret and can be safely sent over an unencrypted (yet trusted) communication channels.
If you do not have anyone else to obtain the fingerprint from, you may need to connect to the server without knowing the fingerprint. Before connecting for the first time, ensure a security of your local machine and a line to the server. For example if you plan to connect to the server from an external site (e.g. from home or a client), but you have a physical access to the server site, connect from the server site the first time (e.g. your workplace).
Once you connect, WinSCP caches the fingerprint and will ensure, that the key is unchanged every time you connect later on.
If you need to know the fingerprint later on for other purposes, like to verify the host key on another machine, or for automation, go to a Server and Protocol Information Dialog. See a Server Host key Fingerprint box.
If you already have the host key cached in the PuTTY SSH client, you can import a PuTTY stored session to WinSCP, including the cached host keys. Make sure the Import cached host keys for checked sites option is checked when importing the sessions.
You can also have the fingerprint displayed in an SSH terminal using
ssh-keygen command (on *nix servers using OpenSSH server):
ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key ssh-keygen -l -f /etc/ssh/ssh_host_dsa_key
A special case is getting host key of a server, that you are an administrator of yourself, yet you do not have a direct secure line to connect through. This is common for virtual servers or servers in a cloud. In such case a server provider should have a specific solution. For example a specialized server in the same private network as your server, with publicly known host keys. You can connect to this specialized server and from it, securely connect to your server (e.g. using SSH terminal). As you are connecting within private network, you can safely trust any host key. Once connected to your server, acquire its host key. With that you can finally connect directly yet securely over a public network. Alternatively, the server provider can provide the host key via some administrative interface. For example see a solution for Amazon EC2, Google Compute Engine or Microsoft Azure.
If you already have verified the host key for your GUI session, go to a Server and Protocol Information Dialog and see a Server Host key Fingerprint box. In the latest beta version, you can have WinSCP generate the script or code for you, including the
-hostkey switch or
In exceptional situations, when security is not required, such as when connecting within a trusted private network, you can use
SessionOptions.GiveUpSecurityAndAcceptAnySshHostKey to blindly accept any host key.
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