Microplastics (MPs) occurrence in farmed aquatic organisms has already been the prime priority of researchers due to the food security concerns for human consumption. A number of commercially important aquaculture systems have already been investigated for MPs pollution but the mud crab (Scylla sp.) aquaculture system has not been investigated yet even though it is a highly demanded commercial species globally. This study reported the MPs pollution in the mud crab (Scylla sp.) aquaculture system for the first time. Three different stations of the selected aquafarm were sampled for water and sediment samples and MPs particles in the samples were isolated by the gravimetric analysis (0.9% w/v NaCl solution). MP abundance was visualized under a microscope along with their size, shape, and color. A subset of the isolated MPs was analyzed by scanning electron microscope (SEM), and Fourier transform infrared spectroscopy (FTIR) for the surface and chemical characterization respectively. The average MPs concentration was 47.5 ± 11.875 particles/g in sediment and 127.92 ± 14.99 particles/100 L in the water sample. Fibrous-shaped (72.17%) and transparent-colored (59.37%) MPs were dominant in all the collected samples. However, smaller MPs (>0.05-0.5 mm) were more common in the water samples (47.69%) and the larger (>1-5 mm) MPs were in the sediment samples (47.83%). SEM analysis found cracks and roughness on the surface of the MPs and nylon, polyethylene, polypropylene, and polystyrene MPs were identified by FTIR analysis. PLI value showed hazard level I in water and level II in sediment. The existence of deleterious MPs particles in the mud crab aquaculture system was well evident. The other commercial mud crab aquafarms must therefore be thoroughly investigated in order to include farmed mud crabs as an environmentally vulnerable food security concern.