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The mtDNA haplogroups of 185 individuals from Native American tribes in Northeast North America were determined. A subset of these individuals was analyzed by sequencing hypervariable segments I and IT of the control region. The haplogroup frequency distributions of populations in the Northeast exhibit regional continuity that predates European contact. A large amount of gene flow has occurred between Siouanand Algonquian-speaking groups, probably due to an Algonquian intrusion into the Northeast. The data also support both the Macro-Siouan hypothesis and a relatively recent intrusion of North em Iroquoians into the Northeast. These conclusions are consistent with archaeological and linguistic evidence.