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An ecosystem-based management fishery is a new way of looking at management of living resources. Trophic levels of basic food items, feeding habits, growth and mortality rate of 20 exploited fish species (including commercial and bycatch) are investigated in the Persian Gulf (from the provinces of Khuzestan, Bushehr and Hormozgan) from 2010 to 2012. The model considers trophic interactions among 12 functional group of the ecosystem involving Phytoplankton, Zeoplankton, Cephalopods, Shrimp, Infauna Benthos, Epifaunal Macrobenthos, Demersal Zoobenthos Feeders, Small Pelagic Planktivorous Fish, Benthoplagic Feeder, Piscivorous, Large Benthic Carnivores And Small Benthic Carnivores. In general 7452 of stomach contents samples were analyzed based on the weight and numerical method and were detected about 40 preys. The results demonstrated gaps in our knowledge on the food web structure. The mean trophic levels were varied from L. klunzingeri (2) to S. tumbil (4.64), while the total catch of some species were fluctuating widely. Result of our study showed that Total mortality varied between 0.45 per year (A. suppositus) to 9.5 per year (P. indicus) and food consumption rate also fluctuated by 1.9 (L. johni ) to 89 (L. lineolatus). The results indicated that some fish species including sardine, Anchovies, small carangids, S. stridens with high frequency in ecosystem, have been occupied in the food web as a wasp-waist. The model showed that most hunters groups live in middle levels in the food web such as N. japonicas, A. latus, P. kaakan, L. nebolusus, P. indicus and T. lepturus . Analysis the catch rate during 2001-2011 reveled that there is a clear trend of declining most of fish species catches in this research except for T. lepturus, P. kaakan and sparids which lead to upset the fundamental ecological balance of the Persian Gulf in future.