There is a phrase that has been attributed to various religious combatants in the moments before merciless slaughter of men, women, and children was to ensue, with the English translation of the original languages going along the lines of "kill them all; God [or Allah, or the Lord, etc] will recognize his own." The earliest instance of that sentiment that I have come across has been pinned on my own Catholic Church, at the time of the Cathar heresy. The Cathars were a group in an area of south/southeastern France, Languedoc, that were a thorn in the side of the Church around the year 1200. Theirs was a sort of resurrection of early beliefs, before official Orthodoxy (literally "right thinking," as opposed to heterodoxy or "different thinking") had been established in the first few centuries after the death and Resurrection of Christ, that Christ was actually of two natures: one divine, and one human. The version of Christianity that won out, however, was that Christ was both human and divine at the same time, rather than one at a time.
One of the main reasons that this group was allowed to exist within Catholic communities (remember that this is hundreds of years before the Protestant Reformation, but even the Reformation did not subscribe to this heresy) and why its membership took off at such an alarming rate was that the Cathars actually exemplified what Christians were "supposed" to be, as opposed to the frequently corrupt and wrong-living clergy and Church holy men of the time. Townspeople were rapidly converting to Catharism, believing that they must in fact be the REAL heirs to Christ's teachings and ways, since they were the ones walking the walk, and the Church was having none of it.
So Pope Innocent III (great name) has this great idea to realize the benefits of a "Crusade," i.e. keeping noblemen and fighting busy while promising them land and other spoils of victory, while accomplishing the goal of stamping out this heresy once and for all. At the city of Beziers, on July 22, 1209, surrounded by a Catholic army of the Pope, the mostly Catholic citizenry refused to turn over their Cathar friends, who were but a small minority in the town, for fear of what the army would do to them (burn them all at the stake as heretics). Upon this refusal, the army entered the town with the order to slaughter the heretics. When the question was raised "how will we know Catholic from Cathar?" the reply came to "kill them all, for God will recognize his own."
Over 10,000 and possibly upwards of 20,000 men, women, and children were put to the sword, and the town was burned to the ground. The "crusade" against the Cathar heresy, called the Albigensian Crusade, would proceed until the goal was accomplished in 1255, with no more people claiming to be Cathars.