Wild castor grows in the high-altitude tropical desert of the African Plateau, a region that has high ultraviolet radiation, strong light and extremely dry conditions. Some genes or alleles persist in the wild castor genome to prevent the species being vanished at extreme condition, but usually be decayed under domestication due to the relaxation of natural selection. To investigate the potential genetic basis of adaptation to both highland and tropical deserts, we generated a chromosome-level genome sequence of the wild castor accession WT05 with scaffold and contig N50 sizes of 31.93Mb and 8.96Mb, respectively. Compared with cultivated castor and other Euphorbiaceae plants, wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair, photosynthesis and abiotic stress responses. Genetic variations associated with positive selection were identified in several key genes, such as LIG1, DDB2, and RECG1, involved in nucleotide excision repair. Moreover, a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments. The identification of the genes and alleles with selection signatures provide insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert, and would serve as targets for directing improvement of modern castor varieties.