Host-associated differentiation (HAD) is the occurrence of genetically distinct, host-associated lineages. Most of the cases of HAD in phytophagous insects have been documented in specialist insects inhabiting feral ecosystems or in generalist parthenogens in agroecosystems. Herein we report HAD in the cotton fleahopper, Pseudatomoscelis seriatus (Reuter) (Hemiptera: Miridae), a native, generalist, non-parthenogenetic insect feeding on native wild hosts [horsemint, Monarda punctata L. (Lamiaceae) and woolly croton, Croton capitatus Michx. (Euphorbiaceae)] and on cotton [Gossypium hirsutum L. (Malvaceae)] in the USA. Examination of genome-wide genetic variation with AFLP markers and Bayesian analyses of P. seriatus associated with three different host plant species at five locations in Texas revealed a geographic pattern of HAD. The geographic pattern of HAD corresponded with differences in precipitation among the locations studied. In three locations, two distinct lineages of P. seriatus were found in association with horsemint and cotton/woolly croton, whereas in two other locations, populations associated with the different host plants studied were panmictic. We suggest that precipitation differences among locations translate into heterogeneity in vegetation distribution, composition, and phenology, which altogether may contribute to the observed geographic pattern of HAD.