The potentially toxic diatom genus Pseudo-nitzschia and particulate domoic acid (pDA) concentrations were investigated weekly to bi-weekly from October 2013 to September 2014 in the Golden Horn Estuary. Pseudo-nitzschia species were detected in 324 of the 666 samples (approximate to 49%). Two species, Pseudo-nitzschia calliantha and Pseudo-nitzschia pungens, were identified based on the scanning electron microscopy examination. A bloom of P. calliantha occurred between May and June, average cell density, 1.1x10(6) cellsL(-1) in May. Pseudo-nitzschia calliantha was commoner than P. pungens almost throughout the study period. They occurred over a wide temperature range (7.4-26.3 degrees C) and moderate salinity (5.9-19.9). The highest cell density occurred at 14.7-19.6 degrees C and 18.5-19.0 salinity, in the lower and middle estuary in winter and late spring. Pseudo-nitzschia species were found in very low densities in the upper estuary, which has variable salinity and low light availability due to high concentrations of suspended material. The pDA concentration in seawater was 0.03-1.0 mu gL(-1). The distribution pattern of pDA coincided with the presence of Pseudo-nitzschia. Pseudo-nitzschia abundance was low in October, when pDA was highest. There was a highly positive correlation between Pseudo-nitzschia abundance and salinity/Secchi depth/pH (p.001), but a negative correlation with inorganic nutrients and Si:N (p<.001). pDA was positively correlated with temperature/salinity and Secchi depth, but negatively correlated with inorganic nutrients (p<.001). Low light availability and highly variable salinity may limit the growth of Pseudo-nitzschia in the upper estuary and the presence of pDA throughout the study area may be related to transport by particulate matter.