Sooting limits of n-hexadecane (n-cetane)/air and 2,2,4,4,6,8,8-heptamethylnonane (iso-cetane)/air mixtures were investigated using a micro flow reactor with a controlled temperature profile at equivalence ratios, ϕ, of 1.5–4.5, inlet mean flow velocities, U0, of 10–100cm/s and atmospheric pressure. Result for n-cetane showed wider ϕ and U0 region of the soot formation than that for iso-cetane. Temperature dependence of mole fractions of polycyclic aromatic hydrocarbons (PAHs) were investigated for n-cetane/air and iso-cetane/air mixtures at ϕ=4.0, U0=2.0cm/s and atmospheric pressure by gas sampling and analysis. At all temperature conditions studied, n-cetane showed higher mole fractions of PAHs than iso-cetane. However, iso-cetane showed higher mole fractions of small alkylbenzenes (toluene, xylene isomers, and ethylbenzene) than n-cetane. Numerical simulation showed the opposite tendency, namely, iso-cetane showed higher/lower mole fraction of benzene/toluene than n-cetane. The species measurement showed branched-chain unsaturated species, 2,4,4-trimethyl-1-pentene (TMP1), was observed in the iso-cetane case at low temperature in which the significant formation of PAHs were not observed, but TMP1 was not observed in the n-cetane case. Considering the molecular structures of the two fuels, branched-chain unsaturated radicals would be formed in the iso-cetane case while those would not be formed in the n-cetane case. The branched-chain unsaturated radicals would play an important role for the formation of the small alkylbenzenes. The capabilities of the micro flow reactor to examine the difference in sooting limits and the PAH formation between rich n-cetane/air and iso-cetane/air mixtures were successfully demonstrated.