The present study deals with the polychaete assemblages inhabiting Polluted soft substrate of the Golden Horn Estuary (Sea of Marmara) and the importance of alien species in polychaete communities. A total of 15 species belonging to 7 families were determined among the benthic materials collected at 4 stations between the depths 4 and 40 in in December 2005. The materials were composed of species tolerant to pollution. Higher diversity and evenness index values were encountered at stations where dissolved oxygen values were relatively high and total organic carbon values were low. The material included four alien species: Desdemona ornata, Ficopomatus enigmaticus, Polydora cornuta and Streblospio gynobranchiata. The most dominant alien species in the area was P. cornuta, with 4340 individuals per square meter. Alien species comprised 46% of total polychaete populations and their distributions were strongly affected by the abiotic factors such as dissolved oxygen, total organic carbon and depth.