Abstract Pangolins are globally threatened by unsustainable hunting for local use and illegal international trade, plus habitat loss. In Benin (West Africa), white-bellied and giant pangolins have experienced a contraction in their distribution areas and population decline during the last two decades. To better understand the factors underlying declines in these species, we investigated extirpation rates of populations over the last 20 years. Because pangolins are elusive species difficult to monitor by standard methods, the status of populations has been assessed through a local ecological knowledge (LEK) approach. We collected information on persistence or extirpation status of pangolins from 156 localities. A binomial model was built to predict population persistence probability as a function of past and ongoing landscape changes, initial abundance (1998), human pressures, and density of the protected area network. The LEK-based model was highly accurate (97% correct classification rate) in predicting the presence of white-bellied pangolin in 52 localities where its presence has been confirmed independently. According to model outputs, persistence probability of pangolins is positively related to distance to main road, initial population abundance, and negatively related to deforestation, shrinkage of favorable habitat, and distance to protected areas. When those factors are controlled for, the white-bellied pangolin has a higher probability of persistence than the giant pangolin. Even assuming no further habitat change, the distribution area of the white-bellied pangolin is predicted to keep decreasing against an unavoidable extinction of the giant pangolin in Benin in the next two decades. Besides validating the usefulness of LEK as a population assessment method, this study emphasizes that, despite a demonstrated positive effect of protected areas, the current situation is not sustainable for pangolins and calls for urgent conservation actions to stop or reduce overhunting.