X-ray diffraction (XRD), transmission electron microscopy (TEM), selected area electron diffraction (SAED), high resolution transmission electron microscopy (HRTEM), environmental scanning electron microscopy (ESEM) and energy dispersive X-ray analysis (EDS) were used in study of starting biomineralization processes in embryos of the sea hare species Aplysia punctata. 10 days old embryos appeared amorphous according to XRD patterns. TEM of the same sample showed that first grains of nanocrystalline dolomite began to form in the amorphous area. The identification of dolomite was confirmed according to TEM dark field images and SAED, as well as by HRTEM. In further development stages of the embryos very faint aragonite rings became visible by SAED. It was shown that the biomineralization process in A. punctata started by formation of the dolomite nanograins which served as centres of crystallization for further aragonite deposition in the larval shell. The creation of unusual intermediate crystalline phase of nano-dolomite in A. punctata embryos is of equal interest for biologist and ecologist as an evolutionary ancestral trait of molluskan biomineralization, as well as for materials scientists, as a promising template in potential bioengineering application and design of appropriate biomimetic routes that could lead to the development of new implantable biomaterials. The discussion of the present results is based on recent knowledge on general biomineralization in mollusks.