Renee C. Jackson is seeing double:

I upgraded to El Capitan and now I have 2 Gmail mailboxes showing in Mail. One is POP and the other is IMAP, and they don’t even show the same number of messages. Same address on “both” mailboxes. How can these be merged?

This is an odd glitch related to the legacy support in Gmail and many mail hosting services for POP (Post Office Protocol) mail retrieval. IMAP (Internet Message Access Protocol) evolved alongside POP, but it’s considered more modern, despite its many drawbacks and inconsistent implementations.

The very tl;dr summary of POP and IMAP is that POP doesn’t interact with a mail server to manage mail folders or how it’s stored; rather, it can retrieve a copy or delete the message remotely. IMAP can replicate the structure of mail on a mail server, and sync back changes, such as deletions or moving messages from one mailbox to another. (If you want to get into more depth than that, it’s an ocean with no bottom. Some companies are working to replace IMAP with a more mature and powerful protocol.)

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