A variety of morphologically different α-MoO3 samples were prepared by hydrothermal synthesis and applied in the selective oxidation of propylene. Their catalytic performance was compared to α-MoO3 prepared by flame spray pyrolysis (FSP) and a classical synthesis route. Hydrothermal synthesis from ammonium heptamolybdate (AHM) and nitric acid at pH 1–2 led to ammonium containing molybdenum oxide phases that were completely transformed into α-MoO3 after calcination at 550 °C. A one-step synthesis of α-MoO3 rods was possible starting from MoO3·2H2O with acetic acid or nitric acid and from AHM with nitric acid at 180 °C. Particularly, if nitric acid was used during synthesis, the rod-like morphology of the samples could be stabilized during calcination at 550 °C and the following catalytic activity tests, which was beneficial for the catalytic performance in propylene oxidation. Characterization studies using X-ray diffraction (XRD), scanning electron microscopy (SEM) and Raman spectroscopy showed that those samples, which retained their rod-like morphology during the activity tests, yielded the highest propylene conversion.