Apple has made some nice changes to the way that message threads are handled in the iOS 10 Mail app, replacing the prior message sub-list with an inline conversation view that users of alternative mail apps and platforms like Gmail will find far more familiar. In addition to presenting all of the messages in a single threaded view, in the Mail app now includes all of the messages in your entire mail account by default, rather than only those in the current mailbox or folder.
Of course, if you don’t like this fully threaded view there are still options to turn it off. The Mail section in the main iOS Settings app now includes a Threading section which, in addition to the global “Organize by Thread” option found in prior iOS versions, now also includes settings to sort threads in reverse chronological order, as well as turn off “Complete Threads” if you want to revert the pre-iOS 10 behavior of only showing messages from the current mailbox/folder in each thread. In the latter case you’ll still get the newer threaded view — there’s no way to go back to the old hierarchical message list design — but any messages that are not contained in the same mailbox/folder as the current message won’t be displayed.
Another handy trick is that swipe options also work in the threaded view on a per-message basis, so you can archive, reply, flag, move, or trash individual messages from within the thread. Just swipe left or right on the message you’d like to take action on, as you would in the normal message list, and the relevant options will appear. Note that Reply and Trash are fixed buttons, while the other buttons will be the same as the ones for the main message list, which can be customized in Swipe Options in your Mail settings.