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Background   Callithrix  marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed here to reconstruct a robust  Callithrix  phylogeny and divergence time estimates, and identify the biogeographic origins of autochthonous and allochthonous  Callithrix  mitogenome lineages. We sequenced 49 mitogenomes from four species ( C. aurita ,  C. geoffroyi ,  C. jacchus ,  C. penicillata ) and anthropogenic hybrids ( C. aurita  x  Callithrix  sp.,  C. penicillata  x  C. jacchus ,  Callithrix  sp. x  Callithrix  sp.,  C. penicillata  x  C. geoffroyi ) via Sanger and whole genome sequencing. We combined these data with previously published  Callithrix  mitogenomes to analyze five  Callithrix  species in total.    Results  We report the complete sequence and organization of the  C. aurita  mitogenome. Phylogenetic analyses showed that  C. aurita  was the first to diverge within  Callithrix  3.54 million years ago (Ma), while  C. jacchus  and  C. penicillata  lineages diverged most recently 0.5 Ma as sister clades. MtDNA clades of  C. aurita ,  C. geoffroyi , and  C. penicillata  show intraspecific geographic structure, but  C. penicillata  clades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainly  C. penicillata  or  C. jacchus  mtDNA haplotypes. The biogeographic origins of mtDNA haplotypes from hybrid and allochthonous  Callithrix  were broadly distributed across natural  Callithrix  ranges. Our phylogenetic results also evidence introgression of  C. jacchus  mtDNA into  C. aurita .    Conclusion  Our robust  Callithrix  mitogenome phylogeny shows  C. aurita  lineages as basal and  C. jacchus  lineages among the most recent within  Callithrix . We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochthonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonous  Callithrix  and autochthonous  C. aurita . Our results encouragingly show that further development of genomic resources will allow to more clearly elucidate  Callithrix  evolutionary relationships and understand the dynamics of  Callithrix  anthropogenic introductions into the Brazilian Atlantic Forest.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07533-1.

Mitogenomic phylogeny of Callithrix with special focus on human transferred taxa