In support of the IOTC ecosystem report card, we estimated several indicators which could be used to measure progress towards monitoring the impacts of IOTC fisheries on and the state of the “Food web/Trophic relationships” ecosystem component. An ecosystem approach requires understanding the ecological effects of removing all animals through fishing. In addition to the monitoring of the total biomass removed, it is also necessary to know the species composition of the total catch and whether they are retained or not, their life history traits and their ecological role in the food web. We used the available fishery statistics and observer data from the EU and Seychelles’ purse seine fishery targeting tropical tunas in the western Indian Ocean to examine the potential ecological effects of this fishery on the food web structure and functioning of this ecosystem. We estimated the total biomass removed by the fishery in terms of weight, trophic level and replacement time by purse seine fishing method (sets on floating objects-FOBs and sets on free schools-FSCs) across different areas in the Indian Ocean.