The co-condensation of 3-iodopropyltrimethoxysilane and tetraethoxysilane with an additional substituted trimethoxysilane (RTMS) in the presence of Pluronic P123 and hydrogen iodide yields bifunctionalized mesoporous silica. The pore size distribution of these materials depends on the nature of the RTMS additive. Excellent results in terms of a narrow pore size distribution were obtained with methyltrimethoxysilane. A particularly interesting bifunctionalized mesoporous material is formed by the co-inclusion of iodopropyl and aminopropyl moieties. The complementary reactivity of these two functional groups is demonstrated by the selective labeling of the amino-iodo-functionalized mesoporous silica with 2-hydroxy substituted nile red and fluorescein isothiocyanate, allowing further characterization of the functional group distribution by confocal laser scanning microscopy.