. Cilia and flagella are the most prominent organelles associated with motility. 2. both are whip like and beat to move the microorganism they differ from one another in two ways. cilia and flagella are very similar in ultrastructure. 3. First, cilia are typically only 5 to 20 m in length, whereas flagella are 100 to 200 m long. 4. Second, their patterns of movement are usually distinctive. 5. Flagella move in an undulating fashion and generate planar or helical waves originating at either the base or the tip. 6. If the wave moves from base to tip, the cell is pushed along; a beat traveling from the tip toward the base pulls the cell through the water.