With the aim of studying ecological specialisation between subspecies, we compared the components of breeding success in individuals of two recently sympatric subspecies, carbo (‘marine’) and sinensis (‘continental’), of the Great Cormorant in a continental colony. The subspecific origin of broods was determined using D-Loop mtDNA and microsatellites. Although there were no differences in clutch size and laying date between the subspecies, mean fledging success was lower for the marine subspecies (–30% according to mtDNA assignment, –38% according to microsatellite assignment) than for the continental subspecies, while mixed breeding pairs had an intermediate fledging success. These results showed that the marine subspecies is less well adapted than the continental one to inland water, which is considered to be the optimal habitat of the continental subspecies. According to these results and to the geographical expansion of the continental subspecies, we suggest that the proportion of marine subspecies in western European inland colonies could decrease when density-dependent competition increases due to saturation.