The main aim of this study was to examine the effects of a polyculture system on the control of the external parasites of western white shrimp, Litopenaeus vannamei. To this end, the western white shrimp postlarvae (PLs) were stocked in nine earthen ponds (600 m2) at a density of 20 PLs m−2 and reared for 4 months. After 40 days of shrimp stocking, Mullets, Mugil cephalus, were stocked at various densities including: control (0 fish/100 m2 pond), treatment 1 (T1: 2 fish/100 m2 pond) and treatment 2 (T2: 4 fish/100 m2 pond). Over the course of the experiment, the external parasites of shrimps were investigated by the preparation of a wet mount from the gill tissue. Based on the obtained results, totally two genera of protozoan parasites, i.e. Zoothamnium sp. and Epistylis sp., were identified over the course of the experiment. In all experimental groups, the incidence and abundance of Zoothamnium sp. was significantly higher than Epistylis sp. (P < 0.05). Also, mean incidence per cent and mean abundance of Zoothamnium sp. and Epistylis sp. were significantly lower in the polyculture treatments (T1 and T2) compared to the monoculture group (control) (P < 0.05). Throughout this experiment, the total organic matter (TOM %) content of the bottom sediments and biological oxygen demand (BOD5 mg L−1) of water samples in the polyculture ponds were significantly lower than the monoculture group (P < 0.05). In contrast, the polyculture ponds had a higher concentration of water dissolved oxygen (O2 mg L−1) compared to the monoculture (P < 0.05). In conclusion, our results show that mullet as a secondary farmed species can reduce indirectly the parasitic pollution of western white shrimp probably through reducing the total organic matters in water and sediments and improving the water quality parameters.