Magnetic fluorescent silica nanotubes were fabricated using reverse micro-emulsions coupled with conventional sol-gel methods. Anodic aluminum oxide templates were used to separate spatially the magnetic and the fluorescent moieties on individual nanotubes and so prevent quenching of the fluorescence. C18 and fluorescent layers were deposited sequentially on silica. Magnetism was then obtained by the introduction of pre-made magnetic nanoparticles inside the nanotubes. The photo- and chemical stabilities of nanotubes were demonstrated through dye release and photobleaching tests. The produced nanotubes did not show fluorescence quenching upon the addition of the nanoparticles, an advantage over conventional spherical fluorescent magnetic nanoparticles. High photostability of nanotubes, magnetism and biocompatiblily make them potentially useful in bioanalysis.