In the early 17th century, French and Portuguese colonizers and Jesuit priests settled in the state of Maranhão and made contact with the Guajajara, an ethnic group that lived along the margins of the Pindaré River. The Guajajara maintained contact with Brazilian national society over the centuries, including with Brazilian admixed populations, and with African slaves that flocked towards the region from the 18th century onwards. The present study investigates the origins of this admixture using mitochondrial genetic variability. The bones of 12 individuals investigated, which are currently part of the collection of the National Museum, were tested for genetic diversity. aDNA was extracted by the phenol-chloroform method and by DNA IQ (Promega, Madison, WI, USA). Amplification of the HVS I region was performed by PCR, followed by direct sequencing using the Big Dye kit (Life Technologies, Foster City, CA, USA). This region was found to represent haplogroups of Amerindians (A, C, and D) and Africans (L, L1b, L1c, and L3). The presence of African haplogroups in Guajajara bones from as early as the 18th century is consistent with historical and anthropological data, suggesting the admixture with Africans and/or Afrodescendants. Therefore, this study demonstrates that women with African haplogroups were introduced into the Guajajara population.