To our knowledge, this is the first study to report the different biodegradation sequences of saturated hydrocarbon compounds by two bacteria— XJ16 and XJ19—using semiquantitative analyses of the gas chromatography–mass spectrophotometry (GC–MS) data of biodegraded oils over 90-day simulation, whcih demonstrating the effects of bacterial species on the biodegradation sequences. The general biodegradation sequence of compounds for XJ16 was similar to that reported previously: -alkanes (most easily to biodegrade) > -alkylcyclohexanes > dicyclic sesquiterpenes > steranes > hopanes. However, the general biodegradation sequence of compounds for XJ19 was different: dicyclic sesquiterpenes (most easily to biodegrade) > steranes > hopanes > -alkylcyclohexanes > -alkanes. The total biodegradation ratios of -alkanes, -alkylcyclohexanes and dicyclic sesquiterpenes by XJ16 were 69.5%, 52.9%, and 48.3% higher than those by XJ19, respectively. The -alkane/-alkylcyclohexane biodegradation sequence for XJ16 and XJ19 were different, but the dicyclic sesquiterpene biodegradation sequences for these two bacteria were the same. However, the total biodegradation ratios of the steranes and hopanes by XJ19 were 12.64% and 18.56% higher than those by XJ16, respectively. For both strains, the biodegradation sequences of some biomarkers were as follows: Cdiastrane > Cdiastrane, C-5α(H)-homopregnane > C-5α(H)-pregnane, βαC20S > βαC20R, αβC20S > αβC20R, αααC20R > αααC20R > αααC20R, Tm > Ts and CM > CH. Moreover, preferential biodegradation of the lower-molecular-weight homologues (C > C > C > C) was observed, with R epimer over the S epimer.