The thermal decomposition of ammonium trimolybdate (NH4)2Mo3O10·H2O, anilinium trimolybdate (C6NH8)2Mo3O10·4H2O and anilinium pentamolybdate (C6NH8)2Mo5O16 in air and nitrogen has been investigated. The decomposition of molybdates was studied in situ by powder X-ray diffraction. Moreover, results of TG, as well as scanning microscopy studies, are presented. It was found that during thermal treatment in air phases of MoOx type are obtained, while thermal treatment in nitrogen leads to obtaining a mixture of MoyCz and MopNq. It is worth noting that even though chemical decomposition and formation of new compounds took place, in some cases needle-like or plate-like shapes of crystallites were preserved during thermal treatment.