Amphiprion percula can grow to 110 mm in length and is often distinguished by three white vertical bars on a bright orange body. The anterior white bar occurs just behind the eye; the middle bar bisects the fish; the posterior bar occurs near the caudal fin. An anterior projecting bulge further characterizes the middle bar. In addition to the white coloring, black edging outlines each fin with varying thickness (Fautin and Allen, 1992; Grant, 1999). Although A. percula’s vibrant colors are eye catching, it is easily confused with Amphiprion ocellaris (false clown anemonefish). One may distinguish the two by counting the number of dorsal-fin spines. A. percula usually has 10 dorsal-fin spines, while Amphiprion ocellaris usually has 11. Also, the latter never has thick black margins outlining the fins (Fautin and Allen, 1992)

There is no difference in color patterns among sexes. Nonetheless, dimorphic variation is present, since the female is larger than the male. Polymorphism, although present in other species of anemonefishes, does not occur in A. percula. Such is the case with melanistic (black pigmentation) variation in some anemonefish species. This is generally absent in A. percula (Fautin and Allen, 1992). (Fautin and Allen, 1992; Grant, 1999)