This study was carried out to measure the concentrations of heavy metals Cadmium and Zinc in muscle of Brachirus orientalis in Bushehr and Asaluyeh seaports during summer 2015. Totally 40 samples of Brachirus orientalis were caught completely at random from Bushehr and Asaluyeh seaports and by the area native fishermen using a trawl net. After biometric measurements of the samples, the muscle of the samples were separated and chemical digestion of the samples was done by MOOPAM, then Cadmium and Zinc accumulation levels in muscles were measured using Graphite furnace atomic absorption instrument (VARIAN AA 100). Based on the obtained results the mean concentrations of Cadmium in muscle tissues of Brachirus orientalis in Bushehr and Asaluyeh seaports were calculated 0.023 ± 0.004 and 0.024 ± 0.006 mg/kg dry weight, respectively. And showed no significant differences in both regions (P>0.05). Moreover, based on the obtained results the mean concentrations of Zinc in muscle tissues of Brachirus orientalis in Bushehr and Asaluyeh seaports were calculated 197.00 ± 111.907 and 224.03 ± 149.377 mg/kg dry weight respectively and showed that there were no significant differences in both regions (P>0.05). The results of this study revealed that the Cadmium concentration in muscle tissues of Brachirus orientalis in studied stations was lower than the levels permitted within the standards of World Health Organization (WHO), Food and Agricultural Organization (FAO), National Health and Medical Research Council (Australia) (NHMRC), Ministry of Agriculture, Forestry and Fisheries UK (MAFF) and Food and Drug Administration (FDA). But Zinc concentration in muscle tissues of Brachirus orientalis in study stations was higher than the levels permitted within the standards.