The main difference is that IMAP (Internet Messaged Access Protocol) always syncs with mail server so that any changes you make in your mail client (Microsoft Outlook, Thunderbird) will instantly appear on your webmail inbox.

On the other hand, in POP3 (Post Office Protocol), your mail client account and mail server are not synced. It means whatever changes you make to your email account in the mail client will not be transferred to the webmail inbox.

So, in simple terms, if you are using IMAP and mark a mail as read, it gets marked as read in your web based inbox too (because the changes are happening on the server). However, this won’t be the case if you are using POP, because the mails are downloaded to your PC and the changes won’t reflect on the server.