AbstractThe metabarcoding of vertebrate DNA found in invertebrate‐derived DNA (iDNA) has proven a powerful tool for monitoring biodiversity. To date, iDNA has primarily been used to detect the presence/absence of particular taxa using metabarcoding, though recent efforts demonstrated the potential utility of these data for estimating relative animal abundance. Here, we test whether iDNA can also be used to reconstruct complete mammalian mitogenomes and therefore bring the field closer to population‐level analyses. Specifically, we used mitogenomic hybridization capture coupled with high‐throughput sequencing to analyze individual (N = 7) or pooled (N = 5) fly‐derived DNA extracts, and individual (N = 7) or pooled (N = 1) leech‐derived DNA extracts, which were known a priori to contain primate DNA. All sources of iDNA showed their ability to generate large amounts of mammalian mitogenomic information and deeper sequencing of libraries is predicted to allow for even more complete recovery of primate mitogenomes from most samples (90%). Sixty percent of these iDNA extracts allowed for the recovery of (near) complete mammalian mitochondrial genomes (hereafter mitogenomes) that proved useable for phylogenomic analyses. These findings contribute to paving the way for iDNA‐based population mitogenomic studies of terrestrial mammals.