Abstract Bottom trawl fishing is the most used worldwide gear generating large amounts of discards due to bycatch of a variety of species. Shrimp fisheries are recognized for their high incidence in global discards. In waters of Patagonia Argentina (43°S - 47°S) an industrial shrimp fishery of high economic value is developed whose target species is the Patagonian shrimp Pleoticus muelleri. The information presented in this study comprises a period of 12 years (2003-2014) and it was gathered by the On-board Observer Program. The Program collects information of all species captured in the fishing fleets. The data analyzed corresponds to the double-rigged otter trawler fleet and the coastal fleet. The fish bycatch composition was characterized in both fleets and the frequencies of occurrence of species and the assemblage areas were analyzed. A total of 101 fish species were identified (59 families) of which 69 were bony fishes, 29 cartilaginous fishes and three species of jawless fishes. The assemblages described correspond to coastal and deep waters, and they are integrated by temperate and subtropical species pointing out the area as an ecotonal zone.