In order to better comprehend the putative association between genotype Trypanosoma cruzi II and primates, an evaluation of the infection in free ranging primates and specimens born in captivity from different geographical areas, the Amazon and the Atlantic forest, was carried out. Seroprevalences of the T. cruzi infection among the primates was similar in both biomes (45.5% and 46%). The parasites were isolated from 8 and 4 different species of primates, respectively from the Amazon and Atlantic forest. Multi-locus enzyme electrophoresis (MLEE) typed the isolates from Amazon as zymodeme 1. Mini-exon gene analysis characterized all these isolates as T. cruzi I, the main genotype circulating in the region. In the Atlantic forest, primates infected with TCI and TCII, as well as a mixed infection (TCI and TCII), were detected. These findings prove that primates may maintain stable infections by both genotypes. Moreover, data show that T. cruzi can occur in a wide range of primate genera, independent of their social behaviour, niches or habitats. Considering the high seroprevalence and stability of T. cruzi infection among the primates, these animals play an important role in the maintenance of the parasite in nature.