Quoting John Corrigan in Early American Studies: First Prejudice: Religious Tolerance and Intolerance in Early America, pages 68–70:

New England thinking about elimination of the [tribes] from the land in the seventeenth century drew upon the Amalek narrative in casting [Native Americans] as evil and the English colonial warriors who battled them as martyrs or prophets.

So, for example, the New England Confederation, in typical fashion, declared war on the Narragansett tribe in 1675 by observing of the “Narrohigansetts and their confederates”: “So Sathan may combine and stir up many of his instruments” in the same way that “Amalek and the Philistines did confederate against Israel.”⁴⁴

At other key moments in the English conquest of the northeastern tribes, sermons and speeches focused on the battlefield leadership of specific persons, much in the same way that English rhetoricians had placed figures such as the Duke of Marlborough at the center of their narratives.

During the [long] eighteenth century, as filiopietistic New England chroniclers were canonizing the heroes of the first generation and bestowing laurels upon the heads of contemporary defenders of the New England way, they also commended [militant colonists] in eulogies and remembrances. Their memories of such persons were of Moses‐like or Joshua‐like heroes who prevailed over evil Amalekites.

And in cases where colonial soldiers died in battle against Native Americans, they were celebrated as martyrs, and in a few instances even though the circumstances of their sacrifice did not immediately suggest heroism, or even competence, in the face of the enemy.

Thus in relating details of the “fight at Piggwacket” in 1725, Thomas Symmes sermonized that Captain John Lovewell, who lost his life, the battle, and a majority of his force bounty‐hunting [Native] scalps, resembled Joshua, Moses’s “Renowned general, in his wars with the Aborigines of Canaan,” the Amalekites.⁴⁵

Just how far the colonial imagination had come in picturing the collective future of Native Americans as empty of promise, as already on course to be blotted out, is redolent in Symmes’s preaching. Offered by Symmes as “a very Celebratory Elegy,” the sermon is grounded in a trust that extermination of the [tribes] was only a matter of time.⁴⁶

That was the faith likewise of Captain Samuel Appleton, who wrote to a friend regarding his rôle as commander of the colonial forces arrayed against the Narragansett tribe in 1675: “By the prayers of God’s people, our Israel in his time may prevail over this cursed Amalek; against whom I believe the Lord will have war forever until he have destroyed him.”⁴⁷

Some nineteenth‐century American writers, looking back on the colonial period, wrote forthrightly about New Englanders’ belief that Native Americans were Amalekites deserving of utter annihilation. In so doing, they read back into the colonial period a nineteenth‐century story about conflict between [Native Americans] and whites as a far‐reaching crusade informed by a cosmic view of good versus evil. That story had its roots in colonial America, but was amplified and refined during the first part of the nineteenth century.

So, the Confederate veteran Robert Lewis Dabney, whose polemical goals were complicated, defended the honor of the South post–Civil War by raising the issue of slavery in the North, that is, “the enslaving of the Indians. The pious ‘Puritan fathers’ found it convenient to assume that they were God’s chosen Israel, and the pagans about them were Amalek and Amorites. They hence deduced their righteous title to exterminate or enslave the Indians.”⁴⁸

[…]

Putnam’s Magazine observed in 1857 that Christians in colonial North American treated [Natives] “as the Amalekites and Canaanites had been treated by the Hebrews.” George Bancroft, in his monumental History of the United States, discerned that New Englanders assumed that they had “a right to treat the [Natives] on the footing of Canaanites or Amalekites.”

The North American Review, remarking on seventeenth‐century English encounters with [Natives] in the northeast, concluded: “Heathen they were in the eyes of the good people of Plymouth Colony, but nations of heathen, without question, as truly were the Amalekites.”

Edward Eggleston looked back in 1883 on the “scenes of savage cruelty” at Mystic in 1637, when a colonial force that had trapped Pequot women and children systematically shot and burned them, a genocide, Eggleston added, that ministers rhetorically justified through “citation of Joshua’s destruction of the Canaanites.” The Living Age likewise observed of the event, “As the Israelites slew the Amalekites, so did the Pilgrims slay the Pequot.”

Bostonian Frederick D. Huntington, who eventually became a bishop of the Protestant Episcopal Church, commented in 1859 that the military exercises against Native Americans in New England were led by men who were “evidently of an energetic spirit and quite an Old Testament cast of mind.”⁵⁰

(Emphasis added.)

Sectarian Christians made similar remarks about Catholics and Mormons. In fact, Corrigan traces the equation of Natives with Amalekites to sectarians equating Catholics with Amalekites.