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Driven from their coastal New England lands during King Philip's War, Pequots and other related Connecticut tribes were resettled in the Mohican territory of Schaghticoke in the 1670s. The Governor of New York felt that an allied tribe in these frontier lands would buffer the Dutch and English settlements against French incursion from the north. A treaty was commemorated in 1676 with the planting of the Witenagemot Oak, which stood behind the Knickerbocker Mansion until the 1940s.

The City of Albany acquired title to "Schaahkook" (Schaghticoke) from a group of Mohicans led by Masahaes and Mahatawee in February of 1707, in exchange for "2 blankets, 12 duffel coats, 20 shirts, 2 guns, twelve pounds pouder, 36 pounds of lead, 8 gallons of rum, 2 casks beer, 2 rolls tobacco, 10 gallons Madeira wine and some pypes," with an annual rent for ten years consisting of "1 blanket, 1 shirt, 1 pair stockings, 1 lapp, 1 kegg rum, 3 pounds pouder, 6 pounds lead, 12 pounds tobacco."

Albany's acquisition opened the area to European settlement. Schaghticoke's agricultural landscape provided the raw material for burgeoning local industry: flax, wool, grains and wood. By the end of the eighteenth century, the Hoosic River was powering wool, cotton and flax mills, a powder mill, flour and and saw mill.

Agriculture - primarily dairy and feed cropping - is still practiced on the rich river bottom land and rolling uplands. Industry has moved away, and the town is a bedroom community of many commuters to the Capital District. Toward the end of summer, the community celebrates its agricultural roots at the annual Schaghticoke Fair.