This paper deals with the precise identification of species of Pseudo-nitzschia, focusing on those which are a potential source of domoic acid, from the Krka River estuary of the Central Adriatic Sea. Domoic acid was measured in phytoplankton net samples and shellfish collected in the winter and early spring of 2011 and 2012. Domoic acid was only detected in early March 2011, both in plankton net samples and shellfish extracts, during a Pseudo-nitzschia species bloom. The measured concentrations of particulate domoic acid (DA) in filtered concentrated seawater varied from 3.1˗6.2 ng DA ml-1. In shellfish sample DA concentration was 0.2 μg g-1. Species belonging to the Pseudo-nitzschia delicatissima complex were more common than those from the Pseudo-nitzschia seriata complex. Morphological analyses by electron microscopy revealed the presence of three potentially toxic species: P. calliantha, P. pseudodelicatissima and P. pungens, and one non-toxic species: P. subfraudulenta. However, P. calliantha and P. pseudodelicatissima dominated during the March 2011 bloom. This study presents the first evaluation of particulate domoic acid along the Eastern Adriatic Sea and the first record of the presence of P. calliantha, P. pseudodelicatissima, P. pungens and P. subfraudulenta in the Krka River estuary.