The French colonists had from the beginning cemented alliances and formed friendships with the Indian tribes of the areas in which they settled, such as the Algonquins, the Innu, the Abenakis, the Mi'kmaq, in the east and the Hurons in the west, from the beginning things had not gone well with the Iroquois, who were centered in lands to the south of Lake Ontario in what later became northern New York State. Their first encounter was in 1609, when, in the company by his Alogonquin allies, on the shores of the lake that later was to bear his name, Samuel Champlain, shot three of their chiefs dead with an arquebus. The immediate results of this startling demonstration of the power of the gunpowder-propelled musket ball was to convince the Indians that they needed firearms as well, which they proceed to acquire, and which were to be a feature of Indian warfare from that point on.
It was not until the 1640s that the Iroquois began to match the French strength. They focused their attentions on the French settlements along the St. Lawrence River, and determined to annihilate them. This grew out of their war with the Huron tribe, with whom they were bitter economic rivals, and with whom the French were allied. The Iroquois war parties moved north towards the St. Lawrence along the Lake Champlain-Richelieu River waterway, which was to remain the main access route for parties intent on invading Canada for nearly the next two centuries, as well as for invasion forces heading south from Canada. They then moved swiftly and silently through the woods until, coming upon an isolated farm or settlement they swooped down suddenly, wielding tomahawk and scalping knife, and usually slaughtering the inhabitants, man, woman, or child. Some, though, might be carried back to the Iroquois homelands, either, usually in the case of women and children, to be incorporated into the tribe, or, usually in the case of men, to be subjected to a slow death by torture.
Some of the greatest heroes of French-Canadian folk memory are of individuals who stood up to such attacks, such as Dollard Des Ormeaux, who died resisting an Iroquois raiding force at the Long Sault at the conjunction of the St. Lawrence and the Ottawa Rivers in May 1660, but succeeded in saving Montreal by his sacrifice. Another was Madeleine de Verchères, who in 1692 at the age of 14 led the defence of her family farm against Iroquois attack.
Although such raids were by no means constant, when they occurred they were bone chilling to the inhabitants of New France, and the colonists felt helpless to prevent them. What at last brought them to a halt, for a protracted period at any rate, was the arrival of a small contingent of regular troops from France, the brown-uniformed Carignan-Salières Regiment, the first group of uniformed professional soldiers to set foot on what is today Canadian soil. After an abortive start in January 1666, led by the aristocrat Alexandre de Prouville, the "Marquis de Tracy" and Viceroy of New France, in September they proceeded down the Richelieu and marched through Iroquois territory burning their crops and homes. The Iroquois sued for peace, which lasted a generation. In the meantime, many from the Carignan-Salieres regiment stayed on in the colony as settlers, significantly altering the colonial demography. They were, after all, hardened veteran soldiers, who before coming to Canada had fought the Turks. They were rough in manners and speech and any hope that local churchmen might have had of fostering a quiet, pietistic society on the banks of the St. Lawrence evaporated. After the departure of the Carignan-Salières regiment in 1667, with the Iroquois temporarily pacified, the colony's administrators at last took steps to form an effective militia organization. Now all men in the colony between the ages of 16 and 65 (excluding the clergy and certain public officials) were issued with a musket and ammunition and became liable for military service.
The war resumed in the 1683 after the governor, Louis de Buade, Comte de Frontenac, attempted to enrich his own fortune by pursuing the western fur-trade with a new aggressiveness, which adversely affected the growing activities of the Iroquois in this area. This time the war lasted ten years and was as bloody as the first.
With renewal of hostilities the local militia was stiffened after 1683 by a small force of regular troops of the French navy, the Compagnies Franches de la Marine. The latter were to constitute the longest-serving unit of French regular force troops in New France. The men came to identify themselves with the colony over the years, while the officer corps became completely Canadianized. Thus in a sense these troops can be identified as Canada's first standing professional armed force. Officers' commissions both in the militia and in the Compagnie Franches became much coveted positions amongst the socially eminent of the colony. The militia together with members of the Compagnie Franches, dressed in the manner of their Algonquin Indian allies, came to specialize in that swift and mobile brand of warfare termed la petite guerre, that was characterized by long and silent expeditions through the forests and sudden and violent descents upon enemy encampments and settlements - in fact the same kind of warfare that was practiced against them by the Iroquois. As they were seen to be urging the Iroquois on, some of the most infamous of these raids were made against settlements in the English colonies, most notably in 1690 against Schenectady in present-day New York, Salmon Falls, New Hampshire, and Portland, Maine. As in the Iroquois raids, the inhabitants were either indiscriminately slaughtered or carried away captive.
The second war against the Iroquois was fought by the French Canadian militia, elements of the Compagnies Franches, some French regular troops sent over especially from France, and by the colony's Indian allies. It was a long and bitter struggle with again French Canadian forces rampaging through Iroquois territory torching their homes and crops. Finally in 1698, increasingly seeing themselves as the convenient scapegoat in what was essentially an English inspired war, the Iroquois sued for peace ending the wars. The signing of the 1701 Grande Paix (Great Peace) in Montreal by 39 Indian chiefs, the French and the English ended the war.
The French, the French Canadians and Iroquois would fight again, but only in the context of the larger French and Indian Wars.