Tunicates are the only animal group known to synthesize cellulose. The current hypothesis is that a horizontally acquired cellulose synthase gene of bacterial origin might have contributed to the establishment of this unique trait. Cellulose biosynthesis in tunicates thus provides an opportunity to understand how a foreign gene was assimilated into a new genome to establish a new trait. Because little is known of the molecular mechanisms underlying cellulose biosynthesis, we set up a practical assessment of cellulose in the ascidian tunicate Ciona intestinalis. We first demonstrated and characterized cellulose in the tunic of adult specimens by chemical purification and by subsequent scanning electron microscopic observation and X-ray diffractometry. Next, we showed that Fourier transform infrared spectroscopic microscopy (FTIR microscopy) can be used to assess cellulose in the small tunic of individual larval specimens without chemical purification. Using FTIR microscopy together with a blastomere isolation technique, we demonstrated that cellulose biosynthesis occurred cell-autonomously in the animal hemisphere of an embryo where the future epidermis, the known site of cellulose biosynthesis, will arise. We combined FTIR microscopy with morpholino antisense oligonucleotide-mediated gene knockdown technology to generate a reverse genetic system to identify genes involved in cellulose biosynthesis. FTIR microscopy was thus able, in combination with current research resources, to contribute to cellular and molecular investigations of animal cellulose biosynthesis.