A mesoporous structure of self-assembled nanocrystals of cubic ZnS doped with Mn2+ ions with a homogeneous distribution of pores of similar size was synthesized at room temperature by a surfactant-assisted liquid-liquid reaction. The component nanocrystals exhibit a high crystallinity and a tight size distribution centered at 2 nm, as well as the narrowest Electron Paramagnetic Resonance (EPR) spectra linewidth and the best resolution reported so-far, effects attributed to self-assembling. The observed EPR spectra consist of lines from the substitutional Mn2+(I) and surface Mn2+(II) and Mn2+(III) centers. Here we show that, in contrast with previous reports, our EPR spectra are highly sensitive to structural changes during pulse annealing in vacuum up to 500 degrees C. The changes are related to the transformation of the surface Mn2+ centers in new Mn2+ centers, attributed to an oxidation process in which the thermal decomposition of the Tween 20 additive, also observed by EPR, seems to be involved. We have also been able to observe, for the first time by EPR spectroscopy, the formation of the ZnO phase and the nanocrystals size increase, which occur during annealing up to 500 degrees C, structural changes confirmed by XRD and TEM observations on the samples previously investigated by EPR.