This has been a popular question, so we wrote a blog post about it.
Message-ID in the original email is included in the
In-Reply-To header in the reply email. So you can use that to track which specific email was replied to.
Mailgun will automatically include a unique Message-ID or you can set your own.
Sinch Mailgun has answers! If you have any concerns or questions, please send us a Support ticket using the Support page within your Mailgun Control Panel. Our Support Team will be happy to assist!