We conducted a population genetic analysis of the two Amazonian tortoises, Chelonoidis denticulata (n = 40) and Chelonoidis carbonaria (n = 39) in a region of sympatry within the Xingú River basin. High levels of gene flow among sampled localities indicated lack of population structure for both species. Genetic parameters indicated a moderate level of genetic diversity in C. denticulata and neutrality tests suggested that populations of this species were in demographic equilibrium with respect to mitochondrial DNA. On the other hand, C. carbonaria presented low levels of genetic diversity and a signal of population expansion. Most records of C. denticulata are from areas of humid forest while those for C. carbonaria are from areas of semi-deciduous forests and transitional areas between humid and semi-deciduous forests. Therefore, the demographic expansion observed in C. carbonaria population could reflect an increase in the availability of suitable habitats for this species due to anthropogenic or natural processes. Additionally, we observed haplotype sharing between these two tortoise species indicating hybridization or incomplete lineage sorting.