Flagella and cilia are both composed of tubulin subunits. despite this similarity, key differences exist between these two structures. for example,

For example FLAGELLA CAN NOT MOVE AS A COORDINATED TEAM, ONLY CILIA CAN MOVE AS A COORDINATED TEAM THUS, THE BEATING PATTERN OF BOTH ORGANELLES ARE DIFFERENT. 
Also, cilia are short and they are usually numerous in number while flagella are long and are usually few in number.