Q:Why do we have denominations when Jesus prayed for the unity of believers?
A: Many people see the existence of denominations as a blot against the church's witness to unity. So they are surprised to learn that denominations were created with quite the opposite intent—to make unity in the church possible. To understand this counterintuitive historical reality, one has to look back 400 years to the century following the Protestant Reformation.
The Reformers had glimpsed a coming day by insisting that the true church could never be identified exclusively with a particular institution (contra Constantine in the fourth century). Still, the Reformers failed to follow this lead; like the Catholics, the Protestants continued to believe that Christian truth held societies together and that only one side in a religious conflict could have the truth. Nonconformity could not be tolerated, and the truth was worth fighting for. And fight they did.
It was not until sheer exhaustion—not victory for any party—brought an end to the religiously motivated Thirty Years War (with the signing of the Peace of Westphalia in 1648) that something of a truce over territorial religion began to take shape. This truce allowed Calvinism to join Lutheranism and Catholicism as a recognized expression of the Christian faith. But this new "peace" retained the territorial concept—those who weren't Calvinist, Lutheran, or Catholic, such as the nonterritorial Anabaptists, or who lived in the wrong territory, continued to be persecuted.
At about the same time in England, the first clear philosophy of denominations was being articulated by the Independents (Congregationalists), who represented the minority voice at the Westminster Assembly ...1