Simulations of aerobic biodegradation have been widely employed to investigate the mechanisms of crude oil biodegradation in geological environments. In this study, a simulated biodegradation experiment was performed with crude oil under aerobic conditions, in which n-alkanes were nearly depleted, thus providing an opportunity to study the biodegradation mechanisms of n-alkanes in crude oils. The sequences of biodegraded oils with a slight to moderate degree of biodegradation were characterized by negative-ion electrospray (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and gas chromatography (GC). Semiquantitative results on the molecular compositions of heteroatom classes were obtained by coinjection of internal standards. The biodegradation mechanisms for n-alkanes and n-fatty acids, as well as some other heteroatomic compounds, are discussed, Evidence from FT-ICR MS and GC analyses of biodegraded oils indicates that n-alkanes can be progressively biodegraded to n-fatty acids through beta-oxidation, or to hydroxycarboxylic and dicarboxylic acids though omega-oxidation. The O-3 class species which have a high relative abundance in the carbon number range of C-33-C-38 with a Double Bond Equivalent (DBE) of 1-3 were assigned and speculated to be bacterial metabolites, which could be a conspicuous indicator of bacterial activity. Neutral nitrogen compounds, such as carbazoles, exhibited a very slight decrease in the stage of biodegradation that was investigated.