A mismatch between the scale of fishery management units and biological population structure can potentially result in a misperception of the productivity and sustainable yield of fish stocks. We used simulation modelling as a tool to compare the perception of productivity, stability, and sustainability of Atlantic cod (Gadus morhua) off New England from an operating model based on the current US management units to a model that more closely reflects the biological complexity of the resource. Two age-structured models were compared: (i) the management unit model, wherein cod were grouped based on the current spatially defined US management areas (Gulf of Maine and Georges Bank), and (ii) the biological unit model, consisting of three genetically defined population components (northern spring spawning, southern winter/spring spawning, and eastern Georges Bank spring-spawning groups). Overall, the regional productivity and maximum sustainable yield of the biological unit model was lower compared with the management unit model. The biological unit model also provided insights on the distribution of productivity in the region, with southern and northern spawning groups being the dominant contributors to the regional spawning–stock biomass and yield and the eastern Georges Bank spawning group being the minority contributor at low to intermediate levels of fishing mortality. The comparison of models revealed that the perception of Atlantic cod derived from the management unit model was of a resource that is more resilient to fishing mortality and not as susceptible to “collapse” as indicated by the biological unit model. For Atlantic cod, one of the main risks of ignoring population structure appears the potential for overexploitation of segments of the population. Consideration of population structure of cod changed our perception of the magnitude and distribution of productivity in the region, suggesting that expectations of sustainable yield of cod in US waters should be reconsidered.