The native form of cellulose is a fibrillar composite of two crystalline phases, the triclinic I(alpha) and monoclinic I(beta) allomorphs. Allomorph ratios are species-specific, and this gives rise to natural structural variations in cellulose crystals. However, the mechanisms contributing to crystal formation remain unknown. We show that the two crystalline phases of cellulose are tailored to distinct structures during different developmental stages of the tunicate chordate Oikopleura dioica. Larval cellulose consisting of I(alpha) allomorph constitutes the body cuticle fin, whereas adult cellulose consisting of I(beta) allomorph frames a mucous filter-feeding device, the "house." Both structures are secreted from the epidermis in accordance with the mutually exclusive expression patterns of two distinct putative cellulose synthase genes. We discuss a possible linkage between structural variations of the crystalline phases of cellulose and the underlying evolutionary genetics of cellulose biosynthesis.