Highly ordered mesoporous crystalline MoSe2 is synthesized using mesoporous silica SBA-15 as a hard template via a nanocasting strategy. Selenium powder and phosphomolybdic acid (H3PMo12O40) are used as Se and Mo sources, respectively. The obtained products have a highly ordered hexagonal mesostructure and a rod-like particle morphology, analogous to the mother template SBA-15. The UV-vis-NIR spectrum of the material shows a strong light absorption throughout the entire visible wavelength region. The direct bandgap is estimated to be 1.37 eV. The high surface area MoSe2 mesostructure shows remarkable photocatalytic activity for the degradation of rhodamine B, a model organic dye, in aqueous solution under visible light irradiation. In addition, the synthesized mesoporous MoSe2 possess a reversible lithium storage capacity of 630 mAh g−1 for at least 35 cycles without any notable decrease. The rate performance of mesoporous MoSe2 is much better than that of analogously synthesized mesoporous MoS2, making it a promising anode for the lithium ion battery.