The incorporation of Mn(II) into the mesoporous material MCM-41, synthesized under acidic conditions with [Si]/[H+] in the range of 0.1 - 0.4 was investigated. Tetraethyl-orthosilicon (TEOS) was used as the silica source and cetyltrimethylammonium chloride or bromide (CTAC/CTAB) as the structure-directing agent. The Mn(II) sites in the final product were characterized by high-field (W-band, 95 GHz) pulsed EPR and electron - nuclear double resonance (ENDOR) spectroscopies that provided highly resolved EPR spectra and detailed information concerning the Mn(II) coordination sphere. These measurements were complemented with X-band continuous wave (CW) EPR and electron-spin - echo envelope modulation (ESEEM) spectroscopies. In addition, the bulk properties of the final products were characterized by X-ray diffraction and 29Si MAS NMR, while in situ X-band CW EPR measurements on reaction mixtures containing the spin probe 5-doxyl stearic acid (5DSA) were carded out to follow the reaction kinetics and the degree of silica condensation. These bulk properties were then correlated with the formation of the different Mn(II) sites. The final product consists of a mixture of two hexagonal phases (d = 38, 43 Å), the relative amounts of which depend on the [Si]/[H+] in the starting gel. Two Mn(II) sites, which exhibit unresolved overlapping signal in the X-band EPR spectra, were easily distinguished in the low-temperature field-sweep (FS) echo-detected (ED) W-band spectra due to their significantly different 55Mn hyperfine couplings. One Mn(II) site, a, is characterized by a hyperfine splitting of 97 G, and the second, b, by 82 G. The relative amount of b increases with increased acidity. Site a is assigned to a hexa-coordinated Mn(II) with water ligands that is anchored to the internal pore surface of the silica either by one coordination site or through hydrogen bond(s). The Mn(II) in site b is in a distorted tetrahedral coordination, located within the first few layers of the silica wall. When the water content of the final products increases, site b assumes characteristics that are very similar to site a, suggesting that the silica wall is 'soft' and not fully condensed. The NMR and in situ EPR measurements show that incomplete TEOS hydrolysis and slow silica polymerization, which occurs for [Si]/[H+] > 0.1, favors the formation of site a, whereas complete hydrolysis and fast polymerization, generating enough acidic Si - OH groups, favors the formation of site b. The incomplete hydrolysis also accounts for the generation of two hexagonal phases.