Spatio-temporal variations of soft-bottom zoobenthic communites in Mersin Bay were examined at seven stations between February and October 2009. A total of 337 species were encountered, of which Polychaeta had the highest number of species (136 species), and Mollusca possessed the highest number of individuals (65% of total specimens) and biomass (59% of total biomass). The highest benthos density (max. 9760 ind. m(-2)) and biomass (max. 133 g m(-2)) were found at shallow-water stations, whereas the highest diversity index values were calculated at the deepest station. The molluscs Cerithidium diplax, Corbula gibba and Bittium reticulatum dominated the area. Changes of zoobenthic communities were spatial rather than temporal and were strongly correlated with depth and the sediment structures. A total of 40 alien species were found in the area, of which 15 species were possibly transported to the area by ships and the others were Lessepsian migrants. The most domiant alien species in the area were C. diplax, Finella pupoides, Notomastus mossambicus and Amphiodia obtecta. Alien species formed dense populations at shallow water stations, and accounted for 12% of total number of species and 31% of total number of individuals in the area. The community parameters estimated for alien species significantly differed among stations but not among sampling periods. The main factors negatively affecting the number of alien species and individuals were depth, the clay percentage and total organic carbon concentration in sediment. The number of native species and individuals in the area show moderate positive correlations with those of aliens.