My mailboxes on my Mac HD have all 'disappeared' since upgrading to el capitan. There were years worth of messages on there and I need the info in a great many of them. How do I get these back?

The mailbox list is divided into categories with headings such as On My Mac. When you hover the cursor over one of those headings (except for Mailboxes), you should see the word Show or Hide on the right. Click Show. The Mailboxes category can't be hidden.

In each category, the mailboxes are arranged in groups, such as Inbox. To the left of each group is a small disclosure triangle. If the triangle points to the right, click it so that it points down.

Note also that you may have to scroll the mailbox list up or down to see all of it.

I had the same problem. I went back to OSX10.10 using the time machine backup I did immediately before the update.

I don't leave anything important on iCloud or email servers. Everything of any consequence is on my Macpro and backed up locally.

I wait with interest to see what the solution is to this problem on OSX10.11!

Sorry not to be more help but for me, the solution is to reject El Capitain until this fault is resolved.

What backups do you have?

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.

Although you can restore messages from a Time Machine snapshot within the Mail application, it generally won't work with messages that were saved by an obsolete version of Mail. In that case, you have to use an alternative method.

Triple-click anywhere in the line below on this page to select it:

~/Library/Mail

Right-click or control-click the highlighted line and select

Services ▹ Open

from the contextual menu.* A folder should open.

Enter Time Machine and scroll back to the snapshot you want to restore from. Inside the folder named "Mail" are subfolders named "V2" and/or "V3" (depending on the version of OS X that was in use at the time the snapshot was taken.) Inside one of those subfolders are more subfolders representing your Mail accounts. The names refer to the email addresses you use. Select the account folders you want and then select Restore ... to... from the action menu (gear icon) in the toolbar of the snapshot window. Restore the folders to the Desktop, not to their original location.

From the Mail menu bar, select

File ▹ Import Mailboxes...

Choose Apple Mail as the format and import from the mailboxes in the folders you restored to the Desktop. The imported messages will appear in a new mailbox. Move the ones you want to keep wherever you like and delete the rest. Then delete the folders on the Desktop.

*If you don't see the contextual menu item, copy the selected text to the Clipboard by pressing the key combination command-C. In the Finder, select

Go ▹ Go to Folder...

from the menu bar and paste into the box that opens by pressing command-V. You may not see what you pasted because a line break is included. Press return.

I just finished restoring all my "On My Mac" mailboxes working off suggestions from Linc and others. Here's what I learned:

1. You may not need to go to a TimeMachine backup. I found that all the contents of my mailboxes were intact and residing in ~/Library/Mail/V3/Mailboxes. I just could not get mail to recognize them.

2. Following on Linc's suggestion I copied the "Mailboxes" folder to my desktop (being careful to copy and not move the folder). You can then import the mailbox files into Mail just as Linc described…BUT there is one little catch. If you have sub-mailboxes they won't be imported. The mailboxes copied to the desktop work similarly to folders in that if you have a sub-box there will be a small arrow next to the top-level mailbox you can click on to see the sub-box. But mailboxes are not really folders so you cannot get to the sub-boxes when using Mail's "Import Mailboxes…". Instead, I copied the sub-boxes to another desktop folder and imported them separately. Once imported I just dragged them to their original position as a sub-box. (Hope I haven't lost anyone)

3. Last step - I went to the Apple Feedback site to complain about the situation. They probably already know about this but I figure the more people who complain, the higher repair priority.

Thank you, thank you!

I had the same issue as KentNeil. I had a large number of messages saved in folders "On My Mac" because of ISP changes. After I upgraded to OS X El Capitan, all of these files vanished! I followed your instructions and was able to recover them. They are no longer arranged the enclosing folders as before, but who cares? I thought that they were lost in cyber space, so I am glad to have them back in a jumble. 🙂

Hello, all. This worked for me. I firstly clicked on all the existing mailboxes & pressed rebuild. Don't worry, nothing happens. I then deleted the mailbox that says 'Today'. All of a sudden all the missing mailboxes "on my imac" reappeared.

Hope this helps.