Cilia and flagella are aimed for similar perpose, motion. And both of them show the (9+2) microtubule arrangement. They are nearly identical in structure. But to be more specific , where exactly does the little difference lie (except the 5-6 bridge) ?
Eukaryotic cilia and flagella are identical in ultrastructure.
The only reason for two different terms for the same thing is historical usage. Traditionally, 'cilia' has been used for shorter, more numerous structures and 'flagella' for longer structures which are fewer in number.
Although cilia and flagella are the same, they were given different names before their structures were studied. Source: Lodish et al (2000)
In fact, some have suggested doing away with this dual terminology, and simply calling all these structures 'cilia'.