Members of St Silas Church took a vote after a process of consultation and prayer.
86 per cent were in favour of leaving the denomination.
The Scottish Episcopal Church recently changed the law to allow same sex marriages to take place in its buildings.
In a statement, St Silas said: “Recent decisions of the Scottish Episcopal Church have made clear to us that the denomination does not regard the Bible as the authoritative word of God.
“With deep sadness, we have therefore decided that for reasons of integrity we can no longer continue as part of the Scottish Episcopal Church.”
In response The Most Rev Mark Strange, Interim Bishop of Glasgow & Galloway said: “Following meetings and conversations with the people of St Silas they have now decided to separate from the Scottish Episcopal Church to fulfil their mission as they understand it to be.
“Although there is always sadness when brothers and sisters walk separately, our brothers and sisters at St Silas continue on their journey of faith with my prayers and blessings; just as they would receive if they decide to return to the Scottish Episcopal Church.”
St Silas is now seeking alternative oversight from the worldwide Anglican conservative group GAFCON.
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