The primary difference between cilia and flagella is how they are organized. Cilia and flagella are both flexible extensions that help cells move.
Cilia and flagella are are structurally similar cell organelles or extensions that aid in cell movement. Cells typically have one or two longer flagella and many shorter cilia. The beating motion of cilia is different from that of flagella, in that flagella move in a wave-like motion and cilia move in a more complicated manner.
A single flagellum might move a cell with a whip-like manner, or two flagella might move in tandem. However, cilia cover most of the body of the cell and beat in a coordinated manner.