Black carbon (BC) is derived from the burning of biomass, a considerable portion of organic matter across terrestrial and marine ecosystems, and a major contributor to global carbon cycles. The benzenepolycarboxylic acid method, which converts condensed aromatic BC structures to molecular markers (BPCAs), has been widely adopted for environmental BC assessments. We present a novel analytical method for the online separation, quantification, and determination of compound‐specific stable carbon isotopes of individual BPCAs via high performance liquid chromatography‐stable carbon isotope ratio mass spectrometry (HPLC‐C‐IRMS). To assess δ13C values of environmental BC, the HPLC‐C‐IRMS method was applied to a variety of samples (soil, char, aerosol, and dissolved organic matter). The method reliably measured amounts and δ13C values of benzenepentacarboxylic acid (B5CA) and mellitic acid (B6CA) over a range of 8.3–130 μmol‐C of organic matter oxidized. BPCA‐specific δ13C values deviated from bulk OC δ13C values for different sample types. However, the stable carbon isotopic composition of B5CA and B6CA was found to be generally correlated with that of bulk organic carbon. The stable isotopic compositions of environmental samples covered a wide dynamic range, indicating BC‐specific δ13C values will be useful for tracking BC sources and processing. For instance, the BPCAs derived from marine dissolved organic matter (DOM) were enriched in 13C relative to BPCAs from riverine DOM, suggesting rivers are not the only source of dissolved black carbon to the oceans.