> What is the difference between cilia and flagella?

There are clear structural differences at microscopic level. they are fueled differently. In short, cilia are like eyebrow hairs, short, weak and simple. They appear in groups of tens or thousands, while flagella are like head hairs, unique or double, rarely more than three, and much longer, thicker and more potent, so faster. Structurally more complex also.

They move in a different way also. Lets say that cilia move like a pendulum and flagella moves like the ribbons in rhythmic Gymnastics