The Church's decision to allow congregations to appoint a minister in a same sex relationship has forced Revd David Macleod and Revd Roddy MacRae to leave.
It's also thought they could be unhappy about plans to lobby for religious observance in schools to be changed to a "time for reflection".
The ministers have now applied to join the Free Church of Scotland.
It means there are now no full-time ministers in Harris, North Uist, Benbecula, South Uist and Wester Ross and part of Sutherland.
16 jobs are being advertised in these areas.
Revd Macleod, said: "Over the past few years I have found myself to be theologically less and less aligned with the Church of Scotland.
"I find myself now to have more in common with other denominations.
"I say this with a heavy heart and with much grief but I do not believe that I can continue in the context in which I find myself."
Revd MacRae, said: "I have been wrestling with this in prayer for quite some time now.
"Although I have a heavy heart, it makes sense to join a denomination with like-minded people where I can be fully supported.
"The Church of Scotland often says it is a broad church, but it has become clear to me that it is not broad enough for Bible-believing Christians."
A Free Church of Scotland spokesman said: "Although we are saddened by the present circumstances in the Church of Scotland, we are happy to provide a home to those who wish to leave.
"We hope that any newcomers to the Free Church will find their new surroundings refreshing and trust they will share our dynamic, vibrant and contemporary mission.
"Over the last five years we have seen a rise in the number of people attending our services, with a particular growth in the number of under 30s. Who says Scotland isn't interested in Biblical Christianity?"
If accepted, Rev David Macleod and Rev Roddy MacRae will bring the total number of former Church of Scotland ministers who have joined the Free Church to 10.