Mytilus edulis and M. trossulus are the two molluscan species co-occurring along the Gaspé coast, eastern Canada. Few studies examine the effects of environmental factors (temperature, salinity, tidal height and wave action) on the local or regional distribution of these two species in areas where they co-occur. This study is designed precisely to examine the niche of each of the two species, particularly in relation to environmental factors in the northeastern part of the Gulf of St. Lawrence, Canada. Mussels were sampled on rocky shores according to a factorial design including six locations, 3 degrees of wave exposure (exposed, semi exposed and sheltered) and 2 intertidal levels (mid and low). Species were distinguished with polymerase chain reaction amplification using a diagnostic DNA marker (Glu-5). Relative frequencies of each species showed no clear patterns of distribution with wave exposure or tidal height. A pattern of distribution at the regional scale does occur, but this pattern could not be related to salinity or temperature gradients observed.