Speciation of plant-feeding insects is typically associated with host-plant shifts, with subsequent divergent selection and adaptation to the ecological conditions associated with the new plant. However, a few insect groups have apparently undergone speciation while remaining on the same host-plant species, and such radiations may provide novel insights into the causes of adaptive radiation. We used mitochondrial and nuclear DNA to infer a phylogeny for 14 species of gall-inducing Asphondylia flies (Diptera: Cecidomyiidae) found on Larrea tridentata (creosote bush), which have been considered to be monophyletic based on morphological evidence. Our phylogenetic analyses provide strong support for extensive within-host plant speciation in this group, and it demonstrates that diversification has involved numerous shifts between different plant organs (leaves, buds, flowers, and stems) of the same host-plant species. Within-plant speciation of Asphondylia is thus apparently facilitated by the opportunity to partition the plant ecologically. One clade exhibits temporal isolation among species, which may have facilitated divergence via allochronic shifts. Using a novel method based on Bayesian reconstruction, we show that the rate of change in an ecomorphological trait, ovipositor length, was significantly higher along branches with inferred shifts between host-plant organs than along branches without such shifts. This finding suggests that Larrea gall midges exhibit close morphological adaptation to specific host-plant parts, which may mediate ecological transitions via disruptive selection.