The new first minister wanted to demote his leadership rival.
He narrowly defeated Kate Forbes and will become Scotland's next first minister.
The SNP minister has doubled down on her controversial stance.
Scotland's finance secretary would not have supported equal marriage as a “matter of conscience”.
The cabinet secretary for finance and the economy is widely seen as a frontrunner in the race to replace Nicola Sturgeon.
Humza Yousaf, Angus Robertson and Kate Forbes are all likely contenders.
Stephen Flynn says the special party conference which was due to debate next steps should be "paused".
The SNP leader's decision to resign could rejuvenate the campaign to break up the UK.
The outgoing leader said the SNP was "awash with talented individuals" who could replace her.
The SNP leader denied she was leaving over "short term issues" such as the transgender rights row.