Technically both the machines are exactly the same but the only difference witnessed is the color options. FZ comes in single shade red or black option whereas the FZ-S has colors like Moon Walk White, Astral Blue, Molten Orange and Cyber Green which makes it more appealing. Also the FZ-S has a crown shaped windshield which is missing in the FZ.

All You Need to Know about Yamaha FZ and FZS Version 2.0 Fi