Both habitat patch size and structure affect the abundance and occurrence of species and thereby can affect the ecology and evolution of species interactions. Here we contrast the level of seed predation and selection exerted by Common Crossbills (Loxia curvirostra complex) and red squirrels (Sciurus vulgaris) in the extensive mountain pine (Pinus uncinata) forests in the Pyrenees with their level of seed predation in two small, isolated forests. Crossbills consumed 5.1 times more seeds in the Pyrenees than in the isolated forests, and six of seven cone traits under selection by crossbills were enhanced in the Pyrenees. In contrast, red squirrels tend to be uncommon in the open mountain pine forests, consuming relatively few seeds in both regions and having limited impact on both mountain pine and the interaction between crossbills and mountain pine. Resident crossbills in mountain pine forests in the Pyrenees have larger bills than in nearby forests, consistent with local adaptation by crossbills and a coevolutionary arms race between crossbills and mountain pine. The mechanisms leading to variation in the interaction between crossbills and mountain pine should be general to many systems because habitat patch size and structure often vary across the range of a species.