Zirconium substituted mesoporous SBA-15 molecular silica with Si/Zr ratios of 10, 20, 40, and 80 have been successfully synthesized at 373 K under microwave-hydrothermal conditions within about 2 h. The degree of framework substitution has been monitored by means of powder X-ray diffraction (XRD), nitrogen adsorption, and UV-vis diffuse, reflectance (DRUV) spectroscopy techniques. Nitrogen adsorption data and XRD patterns confirmed that, the structure, high surface area, and uniform pore size distribution are maintained in the crystallized samples with Si/Zr ratio of 20. Further increase in zirconium loading (Si/Zr = 10) showed the loss of textural properties. The Zr-SBA-15 samples with Si/Zr = 20, 40, and 80 showed a characteristic oxygen to zirconium charge-transfer band at about 210 nm in DRUV-vis spectra consistent with monoatomic dispersion of zirconium in these samples, whereas the presence of a shoulder band at about 240 nm is observed for the sample having Si/Zr ratio of 10 which indicated the formation of zirconium oxide along with SBA-15. These results show that microwave-assisted synthesis is an ideal approach to prepare Zr-substituted SBA-15, which is expected to be useful as a selective oxidation catalyst for reactions involving large molecules.