It has been reported that Atlassian is currently rolling out MarkDown support to it's Confluence application:
"Looking for Markup? We're removing all markup from the editor, and switching to markdown instead. You can still use markup in other parts of Confluence" [SOURCE]
Are there plans to add MarkDown support to JIRA item "comments" ?
I did a search and found that there was a suggestion created for this, JRASERVER-21436, but has been closed as Won't Fix. There is an Atlassian Labs app that someone forked and updated so it work with Jira 7.x.x if you are on server, see JRASERVER-39919
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