M. californianus is the dominant marine mussel species on exposed rocky shores, while M. trossulus is usually the dominant mussel species in more sheltered waters on the west coast of North America. Since these species are physically indistinguishable when small (< 10.0 mm), we developed two polymerase chain reaction (PCR) -based markers to discriminate between them. Using these markers, we identified mussels taken from an exposed coast (n= 114), a sheltered harbour (n= 80), and an upper-intertidal pool (n= 42) on the west coast of Vancouver Island, British Columbia, Canada. M. californianus were found only on the open coast. Small M. trossulus (< 20.0 mm) were common to all three sample sites, but were extremely rare at larger sizes (> 20.0 mm) on the open coast. Our results indicate that M. californianus are excluded from sheltered waters via early life factors, while M. trossulus are excluded from the open coast due to mortality later in life.