A few things here,

1. You are assuming that you are the one that is hacked, it may well be the server that is being hacked and not the machine you are ftping from so contact the admin and notify him/her with the info you have found so far.
2. Change your password to the ftp account (after hearing from the admin) from a (now this is important) **different** machine than you have been using (in case that one is compromised).
3. Make sure that your password is a good password and not easily guessed
4. If possible talk to the admin about installing scp or sftp instead of regular ftp. The ftp program sends passwords in plain text so a simple sniffer will give away your password every time.
5. And finally Contact the site admin. (oh I already said that) well do it again.