At the time of European encounter, the Wolastoqiyik were a primarily agrarian people who supplemented their diets by hunting, fishing and gathering fruits, berries, nuts and natural produce. The French explorers were the first to establish a fur trade with them that became important through their territory. Some European goods were desired because they were useful to Wolastoqiyik agriculture and hunting. The French Jesuits also established missions, where some Wolastoqiyik converted to Catholicism; with years of colonialism, many learned the French language. The French called them Malecites, adapting the name they had been told by other tribes. After defeat in the Seven Years War, the French ceded their territory to Great Britain, including that of the Malecites (without asking their permission).

During the American Revolution, the Malecites were caught between the colonists of New Brunswick, loyal to the British, and rebellious Massachusetts to the south. They were believed to hold the balance of power north of the Bay of Fundy, and both sides vied for their support. Suffering economically because of the decline of the fur trade, the Malecites sought to accommodate both sides rather than fight. Peter Tomah, a Malecite chief and a staunch Roman Catholic, negotiated with the American colonists in council at Machias (Maine) on 27 December 1779. Eventually the tribe split, with Tomah's people allying with the British side.[3]

In the Jay Treaty of 1794, the Maliseet were granted free travel between the United States and Canada because their territory spanned both sides of the border. During the 19th century, intermarriage among the Maliseet and Passamaquoddy and European settlers was common.

When the Treaty of Ghent was signed, ending the War of 1812 and settling the border between Canada and the US, Great Britain ceded a significant portion of the Maliseet/Passamaquoddy territory to the United States. It became part of what is now northern Maine.

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