The whitemouth croaker Micropogonias furnieri is a demersal coastal and estuarine sciaenid fish intensely exploited by small and large scale fisheries in Brazil, Uruguay and Argentina between 22° and 40°S. To study the stocks structure of the whitemouth croaker along southeastern (SEB) and southern Brazil (SB) between 22°28' and 33°53'S, morphometric, meristic and growth data were collected during a bottom trawl survey. Consistent differences between different latitudes were not observed neither for the univariate comparisons of the number of gill rakers and dorsal and pectoral fin rays nor for five morphometric measurements. A principal component analysis of the five morphometric measures did not show a geographical grouping pattern. However, the age structure and growth differed significantly between south and north of Cape Santa Marta Grande (29°S). Former references and this study support the existence of two independent stocks of whitemouth croaker in southeastern and southern Brazil and diverse published studies indicate some degree of mixture between fishes spawning along southern Brazil, Uruguay and Argentina. In terms of access of the fleets there are three jurisdictions: along SB and SEB, where only Brazilian boats fish, in the common fishery zone of Uruguay and Argentina where both countries fish and south of 39°S, where only Argentinian boats can fish but where the whitemouth croaker is not an important target. Efficient management requires the identification of management units based in stocks structure, life history, distribution of the fisheries and jurisdictions. When all these factors are taken into account, excluding local coastal small scale fisheries management, three geographical management units were identified in the shared waters of Argentinian and Uruguayan waters, southern Brazil and southeastern Brazil.