Introduction: Morphological and life-history traits represent characteristics influenced by various environmental factors that can contribute to adaptive variability in many organisms. Temperature is an important environmental factor that drives phenotypic change in different traits in Drosophila (developmental time, fertility, viability, body size, pigmentation, etc.). Therefore, the aim of this study was to investigate the effect of temperature on wing size and shape in two sibling species, Drosophila melanogaster and D. simulans. Methods: Differences in wing size and shape between D. melanogaster and D. simulans flies reared on different thermal regimes were analyzed using a geometric morphometric approach. Both Drosophila species were separately reared on cornmeal–sugar–agar–yeast substrates, at two temperatures (25°C and 19°C), a humidity of 60%, and 12h L–12h D cycle. Wing size and shape were analyzed in 400 individuals (200 individuals per species, i.e., 100 per sex). TpsDig software was used to mark fifteen landmarks per wing picture. The effect of different temperatures on wing shape in both Drosophila species was investigated by Canonical Variate Analysis using the MorphoJ program, while the influence of distinct temperatures on wing centroid size was analyzed in the program CoordGen6. Results: The obtained results indicated that temperature significantly influenced wing shape in males and females in both Drosophila species (p < 0.0001). However, temperature significantly influenced wing centroid size in males and females of D. simulans, which was not the case in its sibling (D. simulans: p = 0.0422; D. melanogaster: p = 0.9994). Conclusion: Based on the results, we can conclude that wing shape is a more variable trait than wing size across temperatures, which could be further related with flying efficiency under different thermal regimes.