The composition and formation mechanisms of the uncharacterized fraction of oceanic particulate organic carbon (POC) are not well understood. We isolated biologically important compound classes and the acid-insoluble fraction, a proxy of the uncharacterized fraction, from sinking POC in the deep Northeast Pacific and measured carbon isotope ratios to constrain the source(s) of the uncharacterized fraction. Stable carbon and radiocarbon isotope signatures of the acid-insoluble fraction were similar to those of the lipid fraction, implying that the acid-insoluble fraction might be composed of selectively accumulated lipid-like macromolecules.