In this study, the geographic and host plant-associated genetic structure of Tomoplagia spp. (Diptera: Tephritidae) was investigated. The study was developed in the rupestrian montane grasslands of the Espinhac ßo Mountain Range, Brazil, where these flies' larvae develop within flower heads of Asteraceae. The three species of Tomoplagia investigated have different host spans within the subtribe Vernoniinae: one is strictly monophagous (Tomoplagia grandis Prado, Norrbom & Lewinsohn) and two are oligophagous [Tomoplagia incompleta (Williston) and Tomoplagia bicolor Prado, Norrbom & Lewinsohn]. The genetic variability and differentiation throughout their geographic distribution were investigated at the local scale (sympatric, between different host species in the same locality) and the regional scale (allopatric, on the same or different host species in different localities). Allele richness was greater for populations of the two oligophagous species. Moreover, population genetic structure was low in all species both on the local and regional scales, and the attribution of individuals of the three species to different genetic groups was not strongly associated with either locality or host plant. These results indicate the absence of simple geographic and host-associated genetic structure in these specialized herbivores, suggesting that females of T. bicolor and T. incompleta have low host philopatry, using various host species indiscriminately within their distribution range. Therefore, the use of host plants by fruit flies of the genus Tomoplagia is a plastic character that can shift temporally and spatially among phylogenetically related and chemically similar plants. Contrary to expectations, given the specialized and intimate nature of their host association, the studied Tomoplagia species showed no clear host-associated genetic differentiation; instead, genetic variation presents a mosaic pattern across hosts and localities.