Inbreeding can have negative consequences on populations and individual fitness, which could be counteracted by inbreeding avoidance mechanisms. The giant panda, a solitary and threatened species, lives in many small populations and suffers from habitat fragmentation, both factors which may aggravate the risk of inbreeding. To evaluate inbreeding level and risk, we performed long-term observations of reproductive behavior, sampling of mother-cub pairs and large-scale genetic analyses on wild giant pandas. Moderate levels of inbreeding were found, but no high-level inbreeding occurred. More significant levels of inbreeding are avoided passively by female-biased natal dispersal rather than by breeding dispersal or active mate-choice mechanisms. The level of inbreeding in giant pandas is greater than expected for a solitary mammal and thus warrants concern for potential inbreeding depression, particularly in small populations isolated by continuing habitat fragmentation.