High quality 3C-SiC nanocrystallites were epitaxially formed on (100) Si wafers covered by a 150 nm thick SiO2 capping layer after low dose carbon implantation and high temperature annealing in CO atmosphere. Carbon implantation is used to introduce nucleation sites by forming silicon-carbon clusters at the SiO2/Si interface acting as nucleation sites for the growth of 3C-SiC nanocrystallites. The formation of the nucleation clusters as well as the morphology, the size, and the density of the nanocrystals were systematically studied by conventional and high resolution transmission electron microscopy. The nanocrystallites were developed following two different modes of growth: The first develops facets along the <100> crystallographic direction giving tetragonal grains and the second facets along the <110> direction resulting in elongated nanocrystallites. The formation mechanism of the nanocrystallites and the strain related with them are also discussed.