The influences of fuel-specific destruction pathways on flame chemistry are determined for two isomeric ester fuels, methyl acetate, CH₃(CO)OCH₃, and ethyl formate, H(CO)OC₂H₅, used as model representatives for biodiesel compounds, and their potential for forming air pollutants is addressed. Measurements are presented of major and intermediate species mole fractions in premixed, laminar flat flames using molecular-beam sampling and isomer-selective VUV-photoionization mass spectrometry. The observed intermediate species concentrations depend crucially on decomposition of the different radicals formed initially from the fuels. The methyl acetate structure leads to preferential formation of formaldehyde, while the ethyl formate isomer favors the production of acetaldehyde. Ethyl formate also yields higher concentrations of the C₂ species (C₂H₂ and C₂H₄) and C₄ species (C₄H₂ and C₄H₄). Benzene concentrations, while larger for ethyl formate, are at least an order of magnitude smaller for both flames than seen for simple hydrocarbon fuels (ethylene, ethane, propene, and propane).