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Pangolins are among the most critically endangered animals due to heavy poaching and worldwide trafficking.However,their demographic histories and the genomic consequences of their recent population declines remain unknown.We generated high-quality de novo reference genomes for critically endangered Malayan (Manis javanica,MJ) and Chinese (M.pentadactyla,MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs.We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units.Demographic reconstruction suggested environmental changes have resulted in a population size fluctuation of pangolins.Additionally,recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load.Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis,which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diets.This comprehensive study-provides not only high-quality pangolin reference genomes,but also valuable information conceing the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities,which is essential for pangolin conservation management and global action planning.