To wrap up the series on religious records, we are in this post looking at the Yukon, Northwest Territories, and Nunavut.
According to the Canadian Encyclopedia entry on the Yukon, 50 percent of the people had no religious affiliation, 46 percent claimed Christian denominations, and 1 percent claimed Native spirituality. There was nothing else listed for the remaining 3 percent. There is a a rather interesting 1990 paper prepared for the Yukon Government on the history of the church in the Yukon. The link to it is here.
The Yukon Archives does have some church records in their holdings. I typed "church records" in the archival descriptions database and got several hits. The collections I clicked on did not have much in the way of actual baptisms, marriages and burials. But, there were photographs, session minutes and journals, among other things in the fonds. They are worth taking a look at too. You never know if your ancestor will be named somewhere, or if you might get lucky and find a photograph.
They have also compiled a pdf of researching genealogy at their Archives. It's 90 pages long but an incredible source of information for them. The link to the pdf is here. The religious records section is on page 25.
The Yukon GenWeb has contact information on their website for Catholic and Anglican church Archives.
The Dawson City Museum does have some church records in their holdings. The link list their collections. Though none state church records specifically, if you click on the each fond, you will find descriptions of each individual collection. I went through and there are three or four collections that include church related records.
According to the Wikipedia page, in 2001 most residents identified themselves as Catholic. The protestant sects were the next largest, and 17 percent stated no religious affiliation. The Virtual Museum has a good overview of the missionary work in the North.
Because the Northwest Territories once included parts of many of the provinces, you may have to look at these provinces to find the records you are looking for. As far as the current boundaries of NWT, there is not much available outside of the Church Archives themselves.
The FamilySearch wiki has contact information for the United and Presbyterian Church Archives that pertain to the Northwest Territories.
The Northwest Territories Public Library has some reference guides available to help you search for records for this area. By enetering "church records" into their online search, I got seven hits, all guides and indexes.
The Hudson's Bay Archives (through the Archives of Manitoba) has a couple of collections related to church records here.
According the the New World Encyclopedia, the majority of residents are Anglican, Catholic, and "Born again Christianity". As with Yukon and the Northwest Territories, there is a history of missionary work here. Click on the link above in the Northwest Territories section for an overview.
Nunavut is a new area, being established in 1999. Before this it was a part of the Northwest Territories, so you will most likely find what you need by looking at NWT genealogy resources.