After upgrading to El Capitan, all my mailboxes have disappeared.

If you're talking about folders you had in iCloud, that is automatically hidden. When you move the cursor over the iCloud header in the left sidebar, you'll see the word "Show" and a + in a circle. Clicking on the + adds a folder, but clicking on show shows you your mailboxes. Hope this is the answer. Scared me to death.😮

I also have this same problem since upgrading to El Capitan on both my MacBook and my iMac and the solution given by dfoy doesn't work for me. Moving the cursor in that area doesn't produce anything - no "Show" and no "+". The mailboxes are still working properly on my iPhone and iPad with iOS 9.0.2 but are completely missing in Mac Mail.

Go to iCloud in System Preferences and make sure Mail is enabled.

Might possibly have got reset.

It's nothing as simple as that unfortunately. The main Inbox still works as normal but all the created Mailboxes (that rules sort mail into) have disappeared. They still exist and appear to work properly on iOS devices.

Found the solution in another forum...

Go to Mail > Preferences > Accounts, and then uncheck the "Enable this account" option and then re-check it.

Sorry, dcr747. This has not worked. All my created mailboxes hhave vanished. The emails that were in them are all in the main inbox, so they are safe, so I guess only solution is to recreate them and them spend a week resorting the emails into their mailboxes.

Not what I expect from a major Apple update!

Same here. My POP3 mailboxes are all gone (although still there on the disk). None of the fixes above worked for me, so I'm going back to Yosemite.

I just figured out how to restore them on my mac. I went into Mail preferences, unchecked "enable this account" on my time warner account. I don't use iCloud for my email, so I only did this for the one twc account. Then I quit mail, waited a few minutes and restarted it. All my mailboxes were now there. I went back into preferences and re-enabled my account. WHEW! Hope this helps someone else.

This happened to me this morning. No updates installed, just all the mailboxes vanished. ...."On My Mac" item was there with an indication that there were 4 new emails and a plus sign suggesting that I could expand it, but it just wouldn't. I tried the "make account inactive, restarting Mail and then making the account active again" but that didn't do it. Mail had been a bit weird last week (I had to change a password to my mail sever for some reason). I assumed it might be just flakiness in the files. So I restarted the computer and things were sorted out.