The analysis of genetic variation in the nucleotide sequences of mitochondrial DNA, provides unique information about the population diversity and human identification. In this study, the mitochondrial DNA sequences of the first hypervariable region (HV-I) were analyzed in 243 unrelated individuals of seven Afro-descendents populations of the Amazon Region. Sequence polymorphisms were detected using PCR and direct sequencing analysis. A total of 133 different haplotypes were found determined by 97 variable nucleotides. Each one of the three more frequent haplotypes was shared by 9 samples and 91 sequences were unique. The genetic diversity was estimated to 0.9898+/-0.0016 and the probability of two random individuals showed identical mitochondrial DNA (mtDNA) haplotypes were 1.2%.