The bloom-forming coccolithophore Emiliania huxleyi (Haptophyta) is a dominant marine phytoplankton, cells of which are covered with calcareous plates (coccoliths). E. huxleyi produces unique lipids of C37–C40 long-chain ketones (alkenones) with two to four trans-unsaturated bonds, β-glucan (but not α-glucan) and acid polysaccharide (AP) associated with the morphogenesis of CaCO3 crystals in coccoliths. Despite such unique features, there is no detailed information on the patterns of carbon allocation into these compounds. Therefore, we performed quantitative estimation of carbon flow into various macromolecular products by conducting 14C-radiotracer experiments using NaH14CO3 as a substrate. Photosynthetic 14C incorporation into low molecular-mass compounds (LMC), extracellular AP, alkenones, and total lipids except alkenones was estimated to be 35, 13, 17, and 25 % of total 14C fixation in logarithmic growth phase cells and 33, 19, 18, and 18 % in stationary growth phase cells, respectively. However, less than 1 % of 14C was incorporated into β-glucan in both cells. 14C-mannitol occupied ca. 5 % of total fixed 14C as the most dominant LMC product. Levels of all 14C compounds decreased in the dark. Therefore, alkenones and LMC (including mannitol), but not β-glucan, function in carbon/energy storage in E. huxleyi, irrespective of the growth phase. Compared with other algae, the low carbon flux into β-glucan is a unique feature of carbon metabolism in E. huxelyi.Electronic supplementary materialThe online version of this article (doi:10.1007/s10126-015-9632-1) contains supplementary material, which is available to authorized users.