The Common marmoset (Callithrix jacchus) and Black-tufted marmoset (Callithrix penicillata) are endemic species in the Northeast, East Central and part of the Northeast, respectively in Brazil. Currently, both species are distributed in different regions of the country, being the main cause the illegal trafficking. The introduction of exotic animals is the second biggest cause of biodiversity loss globally and can lead to hybridization. In Bauru, São Paulo (SP), there is a record of both species and animals showing intermediate patterns between them. Thus, this work aimed to identify individuals of the genus Callithrix present in The Municipal Botanical Garden of Bauru (MBGB) as either pure or hybrids, through morphological and molecular markers. Ten individuals were sampled, 4 of which were pure species for control and six free-living, which were photographed, morphometrically measured, and from which the fragments of the mitochondrial genes COI and D-loop region were amplified. As a result, all animals showed intermediate patterns between both species. After analyzing the sequences obtained for D-loop and obtaining a high haplotypic diversity (h), low nucleotide diversity (π), Tajima D and Fu’s Fs statistic, it is possible to infer that the animals in the area continue receiving gene flow and the population began from a founder effect. Morphological and molecular data indicate that the individuals sampled are hybrids. From the data generated by this research, it is possible to plan the insertion of management of these animals in the Conservation Unit (UC), to avoid population growth and its outcomes.