Oil samples from the Bongor Basin, SW Chad have been geochemically characterized to investigate the biodegradation influence on alkylphenanthrenes. Concentrations of C0-3-alkylphenanthrenes (C0-3Ps) increase markedly after level 6 biodegradation due to the removal of other vulnerable components, decrease sharply after level 7 biodegradation and approach to absence at level 8. Phenanthrene appears to have higher ability to resist biodegradation than C1-3Ps at certain biodegradation levels (≤level 7) due to demethylation, which has been inferred as a possible reaction process during biodegradation of the aromatic hydrocarbons. The enrichment of non-alkylated phenanthrene in biodegraded oils makes biodegradation assessment complicated on the basis of alkylphenanthrene distributions. Individual isomers in alkylphenanthrenes exhibit variable ability to resist biodegradation influence. While certain isomers do show higher ability to resist biodegradation than others, no uniform biodegradation sequence can be established. Meanwhile, the biodegradation susceptibility between hopanes and alkylphenanthrenes varies greatly in different samples. The biodegradation systematics of alkylphenanthrenes proves to be highly complex, which may be indicative of the multiple charges and mixing during biodegradation.