John married Lady Margaret Fleming, Duchess of Albany and Countess of Atholl in 1551 in Blair Castle, Blair Atholl, Perthshire, Scotland. Margaret was born in 1536 in Biggar, Lanarkshire, Scotland; died on 15 Mar 1586 in Kincardine Castle, Kincardine O'Neil, Perthshire, Scotland; was buried on 18 Mar 1586 in Edinburgh, Midlothian, Scotland. [Group Sheet] [Family Chart]

1. Sir John Stewart, 5th Earl of Atholl was born on 22 May 1563 in Dunkeld, Perthshire, Scotland; died on 25 Aug 1595 in Perth, Perthshire, Scotland; was buried on 25 Aug 1595 in Perth, Perthshire, Scotland.
2. Grizel Stewart was born in 1560 in Blair Castle, Blair Atholl, Perthshire, Scotland; died in 1608 in Blair Castle, Blair Atholl, Perthshire, Scotland.
3. Lady Mary Stewart was born in 1566 in Castle Atholl, Perth, Perthshire, Scotland; died in 1588 in Scotland.
4. Lady Isabel Mackintosh was born in 1584 in Atholl, Perthshire, Scotland; died on 15 Sep 1593 in Glenorchy, Dalmally, Argyllshire, Scotland; was buried in Sep 1593 in Glenorchy, Dalmally, Argyllshire, Scotland.