Effective biological treatment of marine wastewater is not well-known. Accumulation of nitrogen and phosphorus from land-based effluent is a crucial cause of red-tide in marine systems. The purpose of the study is to reduce nitrogen and phosphorus in marine wastewater with a pilot plant-scale sequencing batch reactor (SBR) system by using marine sediment as eco-friendly and effective biological materials, and elucidate which bacterial strains in sludge from marine sediment influence the performance of SBR. By applying eco-friendly high efficiency marine sludge (eco-HEMS), the treatment performance was 15 m3 d-1 of treatment amount in 4.5 m3 of the reactor with the average removal efficiency of 89.3% for total nitrogen and 94.9% for total phosphorus at the optimal operation condition in summer. Moreover, the average removal efficiency was 84.0% for total nitrogen and 88.3% for total phosphorus in winter although biological treatment efficiency in winter is generally lower due to bacterial lower activity. These results were revealed by the DNA barcoding analysis of 16s rRNA amplicon sequencing of samples from the sludge in winter. The comparative analysis of the bacterial community composition in sludge at the high efficiency of the system showed the predominant genera Psychromonas (significantly increased to 45.6% relative abundance), Vibrio (13.3%), Gaetbulibacter (5.7%), and Psychroserpens (4.3%) in the 4 week adaptation after adding marine sediment, suggesting that those predominant bacteria influenced the treatment performance in winter.