Environmental change is anticipated to negatively affect both plant and animal populations. As abiotic factors rapidly change habitat suitability, projections range from altered genetic diversity to wide-spread species loss. Here, we assess the degree to which changes in atmospheric composition associated with environmental change will influence not only the abundance, but also the genotypic/phenotypic diversity, of herbivore populations. Using free-air CO2 and O3 enrichment (FACE) technology, we assess numerical responses of pea aphids (Acyrthosiphon pisum) exhibiting a pink–green genetic polymorphism and an environmentally determined wing polyphenism on broad bean plants (Vicia faba) under enriched CO2 and/or O3 atmospheres, over multiple generations. We show that these two greenhouse gases alter not only aphid population sizes, but also genotypic and phenotypic frequencies. As the green genotype was positively influenced by elevated CO2 levels, but the pink genotype was not, genotypic frequencies (pink morph : green morph) ranged from 1 : 1 to 9 : 1. These two genotypes also displayed marked differences in phenotypic frequencies. The pink genotype exhibited higher levels of wing induction under all atmospheric treatments, however, this polyphenism was negatively influenced by elevated O3 levels. Resultantly, frequencies of winged phenotypes (pink morph : green morph) varied from 10 : 1 to 332 : 1. Thus, atmospheric conditions associated with environmental change may alter not just overall population sizes, but also genotypic and phenotypic frequencies of herbivore populations, thereby influencing community and ecosystem functioning.