The diversity and distribution of the diatom genus Chaetoceros (Bacillariophyceae) was studied at monthly, bi-weekly and weekly intervals over two periods (2009-2010, 2013-2014) in the Golden Horn Estuary. Chaetoceros was the most diverse genus in the diatom assemblage of the study area. A total of 23 Chaetoceros species were identified based on light and scanning electron microscopy. Three taxa, Chaetoceros aequatorialis, C. contortus and C. lorenzianus f. forceps were recorded for the first time in Turkish seas. The most common species were C. affinis, C. curvisetus, C. decipiens and C. holsaticus. The contribution of Chaetoceros species to the number of total phytoplankton species was between 15% and 17%. The highest abundance of Chaetoceros species was 507 x 10(3) cells L-1, dominated by C. affinis, C. constrictus, C. holsaticus, C. lauderi in the middle estuary in spring. Chaetoceros species were more abundant in the middle and lower estuary in April and May. In the upper estuary (UE), Chaetoceros species were rarely observed due to low water transparency caused by suspended particulate materials. Light limitation may be considered one of the most important factors affecting the diversity and spatial distribution of these species in the UE. The present work is the first detailed study on the diversity and distribution of Chaetoceros species for Turkish seas.