A study and analysis of the relation of biodiesel chemical structures to the resulting soot characteristics and soot oxidative reactivity is presented. Soot samples generated from combustion of various methyl esters, alkanes, biodiesel and diesel fuels in laminar co-flow diffusion flames are analyzed to evaluate the impact of fuel-bound oxygen in fatty acid esters on soot oxidation behavior.Thermogravimetric analysis (TGA) of soot samples collected from diffusion flames show that chemical variations in biodiesel ester compounds have an impact on soot oxidative reactivity and soot characteristics in contrast to findings reported previously in the literature. Soot derived from methyl esters with shorter alkyl chains, such as methyl butyrate and methyl hexanoate, exhibit higher reactivity than those with longer carbon chain lengths, such as methyl oleate, which are more representative of biodiesel fuels. Structural analysis is performed via Raman spectroscopy on methyl esters derived soot samples and compared with n-dodecane derived soot. These data are consistent with literature reports that lower structural order enhances reactivity. Soot reactivity analysis of methyl esters with different types of carbon-carbon bonds (single versus double), but with the same carbon number, suggests that carbon-carbon bond types and locations also affect soot reactivity. In addition, reactivity of soot from a high-cetane, low-aromatic diesel fuel is assessed and is found to exhibit lower reactivity than soot from a conventional diesel fuel.