Characters—parts, properties, or activities of organisms—can be individuated in multiple, non-equivalent ways. This paper aims to show how these differences matter, to frame the problem of character individuation methodologically, and to outline a path to resolving it. I describe the main scientific roles for the character concept, and analyze three broad approaches to character individuation: functional, descriptive, and developmental. I explore which approaches are appropriate for which roles, and propose two evolutionary hypotheses to explain why functionally and developmentally individuated characters diverge.