A new, 3-D mesoporous amorphous molybdenum-containing silica, denoted Mo-TUD-1, was prepared with variable Mo-loading via direct hydrothermal treatment using triethanolamine as a template. Elemental analysis, N₂ sorption measurements, NMR spectroscopy, XRD, UV-Vis spectroscopy, SEM, HR-TEM, and Raman spectroscopy indicated that as a function of increasing loading, the morphology of Mo changes from isolated sites to nano particulates, and finally to crystalline MoO₃ at a loading higher than 5 wt%. The catalytic performance of the Mo-TUD-1 samples was investigated in the liquid phase epoxidation of cyclohexene with TBHP as an oxidant. Mo-TUD-1 with a low molybdenum loading showed a higher TON as compared to samples with a high loading, suggesting that isolated Mo-sites are more active than particulate MoO₃. Stability and reusability of the catalyst containing isolated sites were also investigated. While leaching was observed initially, stable performance was obtained in as many as three subsequent catalytic runs.