Anastrepha zenildae Zucchi is an important pest in the Semi-Arid region of Rio Grande do Norte and other states in Brazil, with Guava being its main host. Environment induced morphological changes in adult fruit flies can lead to mating incompatibilities among populations within a species. Furthermore, sexual isolation between these populations can be one of the first steps in the speciation process, as described to other tephritid fly species. Here, we compared several body measurements through analysis of variance and geometric morphometrics to assess significant morphological differences between sympatric flies from different hosts: Guava and Jua. We found significant differences in body size for both sexes of flies from the different fruit hosts, with flies from Guava being the larger. Different degrees of sexual size dimorphism of flies from each fruit has also been detected. Flies from different fruits also exhibited different wing shapes, even though the pattern of sexual shape dimorphism remained the same for both fruits. These results show the influence of the host fruits on adult fruit fly morphology, a phenomenon that must be considered when implementing pest control programs such as the Sterile Insect Technique (SIT). Further studies are needed to explore mating preference and genetic structure between these populations.