Background <p>Mitochondrial DNA is a key marker for assessing genetic diversity, critical for the conservation of endangered species. This study investigates the mitochondrial diversity of the Bwindi Impenetrable National Park (BINP) mountain gorilla population (<i>Gorilla beringei beringei</i>), one of the most endangered primate subspecies.</p> Results <p>Using pooled sequencing of 200 faecal samples collected from both habituated and wild gorillas, we identify ten mtDNA variants exceeding a 20% threshold across the population mitogenome. Comparisons with previously sequenced individual BINP gorilla mitogenomes corroborates these findings and reveals additional putative haplotypes, potential heteroplasmy and nuclear mitochondrial DNA segments. Our approach overcomes challenges associated with pooled samples, distinguishing sequencing noise from biological variation. The observed diversity suggests that mitochondrial variability in mountain gorillas is comparable to the higher levels reported in the closely related Grauer’s gorilla (<i>G. beringei graueri</i>).</p> Conclusions <p>This study demonstrates the utility of non-invasive faecal sampling and pooled sequencing for assessing genetic diversity in challenging field conditions, highlighting its potential for population-level genetic monitoring of non-human primates. Our findings provide valuable insights into the genetic makeup of this critically endangered population, contributing to future conservation efforts, and supporting the recovery of mountain gorillas.</p>