Spherical and rod mesoporous silica nanoparticles with hexagonal mesostructure were prepared using the modified Stöber method. The morphology, size and internal pore structure can be controlled by simple changing of surfactant concentration and water:ethanol molar ratio. Monodispersed spheroid MCM-41 was obtained at 40 °C under basic conditions using cetyltrimethylammonium bromide (C16TAB) as template. Obtained materials were characterized by X-ray diffraction (XRD), nitrogen physisorption (BET), transmission electron microscopy (TEM) and scanning electronic microscopy (SEM). The results reveal that the pore volume and surface area increase when the amount of C16TAB increases whereas the pore diameter and particle size decrease. However, the use of ethanol as cosolvent led to an increase in the particles’ size. Moreover, the addition of a 3-aminopropyltriethoxysilane greatly influenced the final particle shape. The material was effectively used for the removal of two fluorescent dyes (Hoechst 33342 and rhodamine 6g) from aqueous solution. Adsorption isotherm models, Langmuir, Freundlich and Temkin were used to simulate the equilibrium data. The Langmuir model was found to fit the experimental data better than others models. Keywords: MCM-41, Modified Stöber method, Adsorption, Hoechst-33342, Rhodamine-6g