The Episcopal Church, a trustee of the land, is now suing the non-denominational church alleging that the parishioners are illegally occupying the space.
The Episcopal Diocese of Long Island believes it is the rightful owner of the property.
"This is where our and they built this church with their own hands and we're just fighting for the legacy of our forefathers," pastor Lawton Bryant said.
In the early 1900s, the land was given to the congregation comprised of native Americans and African-Americans.
The Episcopal church was named a trustee because outright land ownership by those two groups was forbidden.
"This deed is in trust, meaning you're not an owner. You're merely a trustee," attorney Larry McCord said.
"I think it would be a sad day to Wantagh to take the last historical site where it was Native Americans and African-Americans and now wipe that out too," Bryant said.
A spokesman for the Episcopal diocese of Long Island wouldn't say what the diocese wants to do with the land only saying in a statement
The diocese intends to reinvest any proceeds it might realize as a consequence to support ongoing ministry of the episcopal church in the North Bellmore area.
"We don't want to fight but if you push us we will," Bryant said.