recover mail from Time Machine ?

You might want to consider starting a new discussion. Since this one is marked solved and is a couple of years old, less people are likely to look at it. A new post would be much more visible. You can link to this one.

Have you quit and reopened Mail? It should be the normal inbox.

Try re-indexing the mailboxes. This can take awhile if you have a lot of mail.

Reindex messages For El Capitan, try looking in V3. Sierra use V4

Reindex messages (2) See post by Linc Davis

An odd thing to report: For the comfort of my sight, I use a scaled resolution (System Preferences: Displays). When trying to recover an email the screen was truncated so that the 'Restore' button was cut off. There was no apparent way to scroll the screen. Only after going back to 'Default for display' button did I see the 'restore' button. Then I could restore the email for which I was looking. This was on a late 2017 27-inch iMac.

It's May 21st and I'm using Mac OS Sierra and the "Rebuild" option in bookmarks suggestion worked beautifully for me. I had a VIP mailbox disappear after a beta update to Sierra. I thought it would be much more difficult than this. Thank you very much for calling my attention to the "Rebuild" option. I had never noticed that before.

Great suggestion. Anyone with mailbox problems should try that option first.

I also had the same problem, but probably not for the same reason as I use a Mac mini and an external display not made by Apple.
Any way, the solution was rather simple: first, before entering into Time Machine, I reduced the window of Mail to only a part of the screen. And, when in Time Machine, I dragged the bottom of the window up, until I could see the two buttons Restore and Cancel. And if you cannot see the timeline on the right side of the screen, same solution: just drag the right side of the window to uncover it.
Hope this trick will help someone.

First, for the empty Mailbox try: Mail->Mailbox->Rebuild.

If that does not help:

While in Mail, enter Time Machine and you'll be able to restore the mailbox:

1. Make sure Mail is the current app.
2. Open Time Machine.Time Machine displays the current state, indicated as Today (Now), of the selected mailbox in the foreground, with available backups in the background.
3. Use the arrows or the timeline along the right side of the screen to browse through the available backups.
4. Select a mailbox or one or more messages to restore, and then click Restore.Restored mailboxes and messages are organized in a Time Machine mailbox in On My Mac in the Mail sidebar.

Tony:

Your answer above is the gift that keeps on giving! I have a 3TB drive that's been TimeMachine-ing away here for several years, and today I needed to use it.

After messing around for the afternoon, on and off, to recover 3000+ sent messages that disappeared (due to other messing around, long story) -- well, I now understand Time Machine, the restoring part. The messages are all back and neatly tucked in their little folder for the night.

Thanks.

Tom

[Mac user: since '87... Time Machine user: since Sept '14]

I could not find a Time Machine mailbox after running the restore of the messages (2000 or so). Do I have to create it first?

I do not think a late 2017 iMac exists.