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Abstract Malachite Green (MG) dye of the triphenylmethane group is a toxic compound used in the aquaculture industry as an antifungal agent, however, it can accumulate in fish and pose toxicity. The present work aims to remove MG in Microbial Fuel Cell (MFC) as a sustainable and eco-friendly solution. Out of six samples, the highest malachite green degradation was obtained by a sample obtained from Robiki tannery site in agar plates in 24 h at 37 °C. Robiki sample was used to inoculate the anodic chamber in Microbial Fuel cell, the resulting average electricity production was 195.76 mV for two weeks. The decolorization average was almost 88%. The predominant bacteria responsible for MG decolorization and electricity production were identified using 16S rRNA as Shewanella chilikensis strain MG22 (Accession no. OP795826) and formed a heavy biofilm on the anode. At the end of the decolorization process, MG was added again for re-use of water. The results showed efficiency for re-use 3 times. To ensure the sterility of treated water for re-use, both UV and filter sterilization were used, the latter proved more efficient. The obtained results are promising, MFC can be used as recirculating aquaculture system (RAS). The same aquaculture water can be treated multiple times which provides a sustainable solution for water conservation. Graphical Abstract