The difference is a bit of a setup mess for you, but in this instance it does make clear a couple of things. 1. Junk is the messages Thunderbird thinks are SPAM and are managed by Thunderbird junk settings. 2. SPAM is the messages your mail provider thinks are SPAM and on the whole will ignore Thunderbird's settings. Normally you should only have one folder which Thunderbird and you mail provider share for SPAM/Junk mail. The simplest thing is to go into account settings and change the folder used for junk to the SPAM folder. You will still have two folders, but the Junk one should change it's icon to a standard folder icon and can be deleted once you decide the folder has nothing useful in it. Then we get to the truly messy part of SPAM filtering. You can't train your mail providers filter and what it does has nothing to do with Thunderbird. Thunderbird filter is a learning filter. I have not heard of a mail provider having such a thing. They work with one size fits all. Most have some form of whitelisting on their web site, like you have to add the senders to your online address book or the like. Finally the truly messy part. There are "internet security suites" or antivirus products that think they can help manage spam for you and they can add a third independent player in the spam filtering of your email address.