Amdoparvoviruses are increasingly recognized as important pathogens in many small carnivore species. We discovered Red Panda Amdoparvovirus (RPAV) in a zoo-housed cohort of endangered red pandas (Ailurus fulgens), with clinical manifestations ranging from asymptomatic to severe disease. To assess the impact of RPAV in this population, we undertook a cross-sectional and longitudinal fecal shedding study to determine the prevalence, persistence, and genetic diversity of RPAV in zoo-housed red pandas. Virus was detected in feces of 51/101 red pandas (50.5%) from 24/37 zoos (64.8%), and was consistently shed by infected animals over a 3.5-year sampling period. Viral genetic sequences formed a highly diverse but monophyletic group, with multiple distinct lineages and recombinant genomes. These widespread and presumably life-long infections have variable clinical consequences, but the factors mediating this spectrum of outcomes are poorly understood. This study provides critical baseline data for future epidemiology, pathology, and genetics studies, which are needed to understand and ultimately mitigate the impact of RPAV in this endangered species.