The pore structure of mesoporous silica materials synthesized by sol-gel processing can be tailored through the choice of surfactants or polymers templates. The direct incorporation organic groups into the framework of these materials through the incorporation of organic functionalized precursors is also affected by the template. In this work, we demonstrate the direct synthesis of fluorocarbon (heptadecafluoro-1,1,2,2-tetrahydrodecyl and tridecafluoro-1,1,2,2-tetrahydrooctyl) functionalized ordered mesoporous silica. Ordered bi-functional (3-aminopropyl- tridecafluoro-1,1,2,2-tetrahydrooctyl) porous silica have also been achieved. These materials were synthesized using cationic fluorocarbon surfactants, tridecafluoro-1,1,2,2-tetrahydrooctyl pyridinium chloride (FSPCl-1: C₆F₁₃C₂H₄NC₅H₅Cl), heptadecafluoro-1,1,2,2-tetrahydrodecyl pyridinium chloride (FSPCl-2: C₈F₁₇C₂H₄NC₅H₅Cl) and hydrocarbon surfactant cetylpyridinium bromide (CTAB: C₁₆H₃₃NC₅H₅Br) as templating agents. The incorporation of the organic groups is confirmed by FTIR and TGA analysis. The materials' pore order and structure are analyzed using powder X-ray diffraction (XRD) and TEM, and the physical properties are obtained using nitrogen adsorption analysis. Incorporation of the fluorocarbon functional group results in materials of high hydrophobic and lipophobic nature and also high thermal and chemical resistance. These advanced materials have potential application in chromatography, catalysis, sensing, and as gas purification adsorbents. The application of these fluorocarbon functionalized mesoporous silica particles to fluorous phase separation is demonstrated.