The transatlantic slave trade, from the 15th to the 19th centuries, changed dramatically the demography of the Americas. Thousands of enslaved Africans managed to escape from the plantations of European colonizers, and formed independent African settlements of free people (or Marron). Here, I study four Noir Marron communities from French Guiana and Suriname, as well as other populations with noteworthy African heritage in Brazil and Colombia, and West African populations in Benin, Ivory Coast, and Mali. To uncover different population histories, these populations were specifically characterized using different genetic markers based on 17 Y-STRs, 96 Y-SNPs, whole mtDNA genome, and genome-wide SNP data (4.5 million autosomal SNP). The Noir Marron communities revealed a remarkably high African identity, above 98% in all genetic systems analyzed, which is still linked to Bight of Benin region. Both, the Afro-Brazilian and Afro-Colombian populations present different demographic histories because of their different colonial pasts. Within an appropriate historical framework, genetic ancestry can add further understanding of ethnicity in African populations throughout the Atlantic world.