This can happen if you mix IMAP (in Aqua Mail) with POP3 (in another mail app, say Outlook for Windows).

POP3 has no support for marking messages as read or unread. Some mail services mark messages as read once they’ve been downloaded by a mail application, some do not.

IMAP does have support for syncing the read/unread per-message state.

The process is that:

  • a new message arrives, it is initially unread
  • when it’s retrieved with Outlook for Windows (for example) over POP3, the mail service will mark the message as read on the server
  • since POP3 has no read/unread sync, the message will remain unread in Outlook
  • when it is retrieved in Aqua Mail via IMAP the message will show up as read since the Outlook service has marked it such on the server

The solution for this is to not mix POP3 and IMAP. It is recommended to use IMAP when accessing your e-mail from multiple devices/apps as the information is correctly synced between all of them. POP3 should be reserved for more specialised cases and used with knowledge what the protocol can and cannot achieve.