The microtubule axoneme is an iconic structure in eukaryotic cell biology and the defining structure in all eukaryotic flagella (or cilia). Flagella occur in taxa spanning the breadth of eukaryotic evolution, which indicates that the organelle's origin predates the radiation of extant eukaryotes from a last common ancestor. During evolution, the flagellar architecture has been subject to both elaboration and moderation. Even conservation of 9+2 architecture—the classic microtubule configuration seen in most axonemes—belies surprising variation in protein content. Classically considered as organelles of motility that support cell swimming or fast movement of material across a cell surface, it is now clear that the functions of flagella are also far broader; for instance, the involvement of flagella in sensory perception and protein secretion has recently been made evident in both protists and animals. Here, we review and discuss, in an evolutionary context, recent advances in our understanding of flagellum function and composition.