Dinoflagellates are unicellular eukaryotic, mainly planktonic organisms which belong to the protista kingdom. They are widespread in all aquatic environments and some species, when certain conditions are met, may excrete toxins which affect the whole ecosystem and subsequently human health and economy. In unfavourable conditions some species produce cysts, a resistant stage that allows survival. In favourable conditions germination is possible, and thus the formation of new populations which could have negative effects on the environment. The main spreading vector of dinoflagellate cysts are ballast waters. In this study sediment samples from the Kvarner and Rijeka bay collected in summer and winter of 2015. were analized. 27 mophotypes were identified with Lingulodinium polyedrum and Gymnodinium/Biecheleria/Scrippsiella complex being the most abundant in summer and Protoperidinium sp. and Gymnodinium/Biecheleria/Scrippsiella complex in winter. Temperature and the distance from port affect the cyst abundance the most. Spreading of the cysts from the port of Rijeka towards Kvarner and Rijeka bay has been observed. Higher cyst abundances were found on the pier and adjacent stations, alas, in this study it was not possible to conclude whether the higher abundances were due to higher production of cysts from the water column or ballast water discharge.