Introduction:Cinnamon is dietary part of almost every Indian, hence there is no harm to consume it or apply it as antibacterial agent. Herein, we have observed that 0.5, 0.6 and 0.7 % concentrations cinnamon essential oil sufficient to control A. hydrophila within 5hrs of exposure. Cinnamaldehyde of is major component of used essential oil which has targeted the Flgn, Fij and Flja protein of flagella flowed by inhibition of swimming motility. Cinnamaldehyde was associated with damaging of cell membrane and leakage of electrolytes in extracellular environment.Aim of the study:In the current study cinnamon essential oil has been used to control the growth of multiple drug resistant A. hydrophila. A. hydrophila was isolated from well water system, and it was imipenem resistant bacteria as well. Materials and Methods: Cinnamon essential oil was characterized by using HPLC and FTIR. Antibacterial killing mechanism was determined by using electrical conductivity test, cytotoxic test by MTT assay, cell wall integrity test and motility test. Results:Cinnamon essential oil has potential to control the growth of A. hydrophila, and complete inhibition of cells was observed within 5hrs of exposure to 0.7% concentration of essential oil. By motility test and molecular docking it has been confirmed that for killing of bacterial cells, cinnamaldehyde of cinnamon essential oil targeting the cell membrane proteins as well as flagellar proteins Flgn, Fij and Flja.