Genetic diversity is recognized as one of the three forms of biodiversity that deserves global conservation attention, as it is linked to the species capacity to adapt to changing environment. Low levels of genetic diversity can result from historically low population sizes and are not directly informative about the species evolutionary potential. Therefore, evaluating temporal changes in genetic diversity is crucial for devising effective conservation plans. Here, we focus on the understudied Grauer s gorillas endemic to the eastern Democratic Republic of Congo. The distribution range of this endangered great ape has been heavily impacted by war and instability for the last several decades, resulting in documented but unquantified population decline in Grauer s gorillas. To disentangle the effects of historical demographic and recent anthropogenic events, we use target DNA capture methods to characterize complete mitochondrial genomes in >40 contemporary fecal samples from two Grauer s gorilla populations and 50 up to 100-years old museum-preserved specimens. This temporal approach allows us to investigate changes in genetic diversity, population fragmentation and prevalence of female-mediated gene flow during the last century. By making non-invasive fecal samples amenable to target DNA capture and next-generation sequencing approaches, our study opens doors for large-scale investigations of cryptic and endangered wild populations of primates and other mammals.