Carbon isotope (δ13C) records from marine sediments have been extensively used in Cenozoic chemostratigraphy. The early Paleogene interval in particular has received exceptional attention because negative carbon isotope excursions (CIEs) documented in the sedimentary record, e.g. at the Paleocene Eocene Thermal Maximum (PETM), ca ~56 Ma, are believed to reflect significant global carbon cycle perturbations during the warmest interval of the Cenozoic era. However, while bulk-carbonate δ13C values exhibit robust correlations across widely separated marine sedimentary sections, their absolute values and magnitude of CIEs vary spatially. Moreover, bulk-carbonates in open-marine environments are an ensemble of different components, each with a distinct isotopic composition. Consequently, a complete interpretation of the bulk δ13C record requires an understanding of co-evolution of these components. In this study, we dissect sediments, from early Paleogene interval, at ODP Site 1209, Shatsky Rise, Pacific Ocean to investigate how an evolving bulk-carbonate ensemble influences the overall carbon isotope record. A set of 45 samples were examined for δ13C and δ18O compositions, as bulk and individual size fractions. We find a significant increase in coarse-fraction abundance across PETM, driven by a changing community structure of calcifiers, modulating the size of CIE at Site 1209 and thus making it distinct from those recorded at other open-marine sites. These results highlight the importance of biogeography in marine stable-isotope record, especially when isotopic excursions are driven by climate- and/or carbon-cycle changes. In addition, community composition changes will alter the interpretation of weight percent coarse fraction as conventional proxy for carbonate dissolution.