HgSe nanorods have been synthesized through a simple hydrothermal reduction approach. The nanorods formed were ≈45 nm average diameter and ≈3 μm nm in length. X-ray diffraction characterization suggested that the product consists of cubic phase pure HgSe. The as-prepared products were also characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). An X-ray energy dispersive spectroscopy (EDX) study further confirmed the composition and purity of the product. The synthesis procedure is simple and uses less toxic reagents than the previously reported methods. The results showed that the capping agent CTAB (cetyltrimethylammoniumbromide) plays a crucial role in the process. Other factors, such as the reaction time, temperature, different capping agent and the reductant type also have an influence on the morphology of the final products to some extent.