The solid-electrolyte-interphase (SEI) layers formed on the electrodes of pristine Si and carbon-coated Si (C-Si) particles in Li cells have been studied. The counter electrode is Li, and the electrolyte is LiPF6 in the mixture of ethylene carbonate and ethyl methyl carbonate. Other than those, such as Li carbonates and fluoride, already known to the SEI of graphite electrode, there were detected significant amounts of SEI species unique to each of the Si electrodes. On the pristine Si electrode, there was concurrence of abundance of C and Si fluorides after long cycles. Coating the Si particles with a graphitized carbon layer has significant effects on the SEI formation. It helps to keep the Si particles remaining integrated after cycling, resulting in a smooth superficial SEI layer. It removes the native oxide layer not only to reduce humidity contamination but also to significantly change the SEI compositions. The SEI of the C-Si electrode shows the absence of Si and C fluorides but the presence of siloxane species. Reaction mechanisms leading to the formation of the fluoride and siloxane species have been proposed, elucidating an important role played by the native Si oxide layer.