ABSTRACT: Changes in species abundances caused by climatic variability have long been linked to alterations in community composition, species interactions and maintenance of biodiversity in marine ecosystems. Here we use multivariate regression tree (MRT) analyses to quantify how changes in species abundances and environmental variability contributed to observed patterns of community composition in the Gulf of St. Lawrence during 2 contrasting periods (the cooler and less saline period 1991 to 1995 and the warmer and more saline period 1997 to 2003). Broad-scale patterns of community composition in both periods were consistently explained by the depth and salinity of the benthic environment, but biological factors differed. In the cold period, the previous year’s catches of snow crab Chionoecetes opilio and northern shrimp (mainly Pandalus borealis) were most important, while in the warm period the previous year’s catch of Atlantic cod Gadus morhua dominated. MRT models further identified spatially discrete areas where communities are characterized by relatively high abundances of these species. These results indicate that environmental variability leads to dynamic and spatially explicit responses not only of single species, but of marine communities. Applications of ecosystem management in the face of climate change must take this into account.