Anaerobic digestion (AD) experiments were conducted on an industrial algae strain of Nannochloropsis salina in two identical 5-liter digesters for about 300 days. One digester was fed with whole cell algal biomass (WCB) while another with lipid-extracted algal biomass residues (LEB). WCB digester shows higher specific methane productivity ranging from 0.59 to 0.65 m(3) CH4/kgVS, while that in LEB digester ranges from 0.29 to 0.42 m(3) CH4/kgVS. Results show that organic loading rate (OLR) in LEB digester can reach up to 5.0 gVS/L/d, and WCB digester failed at that of 3.0 gVS/L/d since long-chain fatty acids (LCFA) were identified as the main inhibitor during AD of algal biomass. At these two maximum OLR, both WCB and LEB digester could achieve a volumetric methane production rate of 1.40 m(3) CH4/m(3)/d. Illumina MiSeq sequencing targeting 16S rRNA genes revealed that Proteiniclasticum, Tissierella, Methanosaeta and Methanomethylovorans were dominant genus at low OLR, while Trichococcus, Levilinea Methanosaeta and Methanobacterium dominated under high OLR. Furthermore, population shifts in methanogenic archaeal communities to Methanobacterium in WCB digester were noticed as aceticlastic methanogens are more sensitive to LCFA than hydrogenotrophic methanogens. (C) 2021 Elsevier Ltd. All rights reserved.