Molecular characterization of pyrogenic organic matter (PyOM) is of great interest to understand the formation and behavior of these increasingly abundant materials in the environment. Two molecular marker methods have often been used to characterize and trace PyOM: polycyclic aromatic hydrocarbon (PAH) and benzenepolycarboxylic acid (BPCA) analysis. Since both methods target pyrogenic polycyclic compounds, we investigated the linkages between the two approaches using chars that were produced under controlled conditions. Rye and maize straws and their analogues charred at 300, 400 and 500 °C, respectively, were thus analyzed with both methods. Moreover, we also measured BPCAs directly on the lipid extracts, on which PAHs were analyzed, and on the respective extraction residues, too. Both methods revealed important features of the chars, in particular the increasing degree of aromatic condensation with increasing highest heating temperature (HTT). The overlap between the two methods was identified in the lipid fraction, where the proportion of benzenetricarboxylic acids (B3CAs) correlated with PAH abundance. The results confirmed the validity and complementarity of the two molecular marker methods, which will likely continue to play a crucial role in PyOM research due to the recent developments of compound-specific PAH and BPCA stable carbon (d¹³C) and radiocarbon (¹⁴C) isotope methods.