Bottom trawling is important in Brazilian fisheries and is currently highly multi-specific due to the overexploitation of the original targets; unselective fishing method; very large permitted fishing area and the country's high marine biodiversity. Fishing licensing in Brazil was modified in 2012 and is now based in five criteria: target species; "expected by-catch"; "incidental catches"; fishing method and area of operation. Licenses of trawling fleets exhibit, therefore, dozens of species catchable under the first three criteria. In this paper, we analyze industrial double-rig trawling fleets targeting shrimps and demersal fishes, in order to verify in what extent the new system adhere to the current fishing reality, giving new information to improve the current management regime. A total of 4,194 trips from 191 vessels were studied between 2008 and 2010 in southern Brazil. In spite of depending economically on their targets, the fleets are formally authorized to catch a high percentage of species in common (41 to 71%), and the actual landings revealed an even greater overlapping among them (71 to 82%). Vessels licensed to catch demersal fishes obtained nearly 50% of their revenue from items not included in their licenses. It was concluded that the current system encourages excessive effort concentrations over fishing resources, as they can be legally caught by most vessels irrespective of their licenses. It is suggested that licensing should move from a species-based to a spatial-based approach, by defining smaller management areas according to the respective species assemblages. Landing composition would be, therefore, mostly a biological and technological consequence, making management more reasonable and workable under a multi-specific and mega-diverse scenario.