javascript:void(0) The boll weevil, Anthonomus grandis grandis Boheman, and thurberia weevil, Anthonomus grandis thurberiae Pierce (Coleoptera: Curculionidae), together comprise a species complex that ranges throughout Mexico, the southwestern regions of the United States, and South America. The boll weevil is a historically damaging and contemporaneously threatening pest to commercial Upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), whereas the thurberia weevil is regarded as an innocuous non-pest subspecies that is mostly found on non-cultivated Gossypium species, e.g. Thurber’s or Arizona cotton, G. thurberi, throughout its native range in western parts of Mexico and the southwestern US. Recent independent analyses using mitochondrial COI and whole genome ddRADseq have suggested the independent evolution of these lineages is largely attributable to geographic isolation and not to host plant preference. We furthered this investigation by employing comparative genomic, population genetic, and pangenome methodologies to identify large and small polymorphisms within this complex and described their role in demography and adaptation. We also leveraged genetic differences to identify nearly 40,000 diagnostic loci between the subspecies, find genes under selection, and model the subspecies’ shared and unique evolutionary history. Interestingly, structural variations capture a large proportion of genes at the population level and demographic reconstruction suggests a split between these subspecies that coincides with cotton cultivation in the southern U.S. in the late 1800s. Observed polymorphisms are enriched for reproductive, regulatory, and metabolic genes which may be attributed to the boll weevil’s rapid expansion onto commercial cotton.