Abstract Aquatic weeds including submerged macrophyte have been excessively propagated and causing environmental issues in freshwater environment of many countries, and the sustainable treatments have been investigated. In the present study, five submerged macrophyte species dominant in Lake Biwa, Japan, Ceratophyllum demersum, Egeria densa, Elodea nuttallii, Potamogeton maackianus and Potamogeton malaianus were used as a substrate for anaerobic digestion to investigate the chemical composition and the anaerobic digestibility. The lignin content of the submerged macrophyte widely ranged from 3.2 to 20.7%-TS depending on species. The lignin of all macrophytes contained 27.2–59.4% of hydroxycinnamic acids, suggesting they are relatively alkali-labile as compared with woody plants. The total CH 4 yield of submerged macrophytes greatly varied from 161.2 to 360.8 mL g-VS −1 depending on species. The CH 4 conversion efficiency of C. demersum , El. nuttallii , Eg. densa , P. maackianus and P. malaianus was 57.1, 61.4, 60.6, 33.9 and 72.2%, respectively. The results showed that C. demersum , El. nuttallii , Eg. densa and P. malaianus are feasible for anaerobic digestion due to the high methane recovery, whereas P. maackianus was not preferable for anaerobic digestion. The present study revealed that the methane recovery of submerged macrophytes is regulated by the lignin content, as well as other lignocellulosic biomass.