In this work one-pot microwave assisted synthesis of selenium nanoparticles by decomposition of cyclo-octeno-1,2,3-selenadiazole in the presence of oleic acid and diphenyl ether is described. Three different forms of Se nanoparticles i.e. red, black amorphous and crystalline red were synthesized by varying the reaction time with microwave irradiation. The formation of Se nanoparticles from such a microwave reaction was monitored by UV-Visible spectroscopy at specific intervals. X-ray diffraction (XRD) measurement and Raman spectroscopy confirmed the trigonal crystal structure of the Se nanoparticles so-isolated. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) showed the globular morphology of the red and black Se particles. The particle size distribution was found to be between 1–20 nm for red Se. Thermogravimetric analysis (TGA) revealed a decomposition range between 180–240 °C leading to the possibility of interconversion of the crystal structure. A %wt loss between 94-99% was observed for various forms of Se.