The first inhabitants of what is now known as the Quoddy area were the Passamaquoddy People who lived in small, mobile groups and gathered and hunted in a land that had only recently been freed from the grip of a massive continental ice sheet. Archeologists call this period the Paleo-Indian phrase. Sites of these original pioneers have been found at several locations in Maine and New Brunswick. The fluted points characteristic of Passamaquoddy hunter-gatherers have been found in the vicinity of Calais/ St. Stephens and in the upper part of the St. Croix River drainage, near West Grand Lake.

During the next several millennia, the environment of the Quoddy area, and of the Northeast in general, changed and became more similar to that of the present. During his period, known as the Archaic, Passamaquoddy people developed patterns of subsistence and settlement some of which persisted into the 17th century. The Archaic period w i t n e s s e d t h e g ro w t h o f Passamaquoddy populations, and the development and florescence of several cultural traditions. The period provides archeological evidence of an increase in the expression of ritual, particularly in the burial of the dead, and the earliest evidence of the use of marine resources in the Passamaquoddy Bay region.

St. Croix Island contains cultural remains of Passamaquoddy occupations dating back 3,000 years to the Ceramic Period. The culture of this region during that time is known as the Quoddy tradition. Archeological remains of this culture abound along the estuaries bays, and many islands of the Passamaquoddy Bay area. Quoddy tradition sites typically are located near the waters edge and contain a midden area near the water with a habitation area further back from the beach. The dwellings appear to be single-family wigwams built over shallow depressions. Many shell middens date from this period. They bear evidence of an economy strongly oriented toward the sea, at least seasonally.