The Bishop of Moray, Ross and Caithness replaces Most Rev David Chillingworth who retired this year.
Speaking about his new role, he said: "I am humbled by the confidence shown in me by my colleagues and I will seek to serve the church as Primus with love and strength.
"I am deeply privileged to be the Bishop Moray, Ross and Caithness and am very aware that it has been 82 years since a Bishop of Moray became Primus.
"I pray that I may be worthy of this trust.
"I will continue to serve in my beloved highlands while I also step out into new and exciting journeys of faith in both Scotland and the wider international church."
Bishop Mark is the youngest member of the College of Bishops and was consecrated Bishop of Moray, Ross and Caithness in 2007.
He's served the church in England and Scotland.
The appointment comes just weeks after the Scottish Episcopal Church voted to permit same sex marriage.
One of Bishop Mark's first jobs will be to attend the forthcoming Primates Meeting in Canterbury, where the Church's decision is expected to be on the agenda.
In the last Primates meeting, the US Episcopal Church was reprimanded for a similar move.