The anaerobic degradation of petroleum is an important process in natural environments. So far, few studies have considered the response of the microbial community to nanomaterials during this process. This study explored the potential effects of graphene oxide and biochar on the anaerobic degradation of petroleum hydrocarbons in long-term experiments. Cyclic voltammetry and electrochemical impedance spectroscopy indicated that the addition of carbon based materials promoted the electrochemical activity of anaerobic cultures that degrade petroleum hydrocarbons. The maximum degradation rates for benzene, toluene, ethylbenzene, and xylene (BTEXs) in the cultures incubated for 10 weeks with graphene oxide (0.02 mg/L) and biochar (20 mg/L) were 76.5% and 77.6%, respectively. The maximum degradation rates of n-alkanes in the cultures incubated for 10 weeks with graphene oxide (2 mg/L) and biochar (100 mg/L) were 70.0% and 77.8%, respectively. The 16S rDNA copy numbers in the treatments with 0.02 mg/L graphene oxide and 20 mg/L biochar were significantly higher than others during the process (P < 0.05). In the 2nd week, the maximum copy numbers of the masD and bamA genes in the treatments with biochar were 349 copies/mL (20 mg/L) and 422 copies/mL (20 mg/L), respectively, and in the treatments with graphene oxide were 289 copies/mL (0 mg/L) and 366 copies/mL (0.02 mg/L). The contents of carbon-based materials had slight effects on the microbial community structure, whereas the culture time had obvious effects. Paracoccus denitrificans, Pseudomonas aeruginosa, and Hydrogenophaga caeni were the dominant microorganisms in the culture systems under all treatments. (C) 2019, The Society for Biotechnology, Japan. All rights reserved.