The cosmopolitan diatom family Chaetocerotaceae abounds in the phytoplankton of coastal regions, comprising ca. 170 species, belonging to two genera, Chaetoceros and Bacteriastrum. In the Adriatic Sea the group is ecologically important represented with ca. 50 species whose identification is often problematic. The species morphology was assessed by analysing the material from cultured strains and the field plankton samples collected at 8 locations along the eastern Adriatic coast from 2006 to 2012. All taxa were studied with light, scanning and transmission electron microscopy. Ecological relationships were investigated: (i) in the coastal area of northern Adriatic (biweekly in 2008 – 2009) (ii) in Krka River estuary (twice a day during six days in July 2010). 49 morphologically distinct taxa were recorded, of which six were affiliated with the genus Bacteriastrum and 43 with genus Chaetoceros with 41 species, two varieties, two tentatively identified and four unknown morphotypes. Five taxa have been reported for the first time for the Adriatic and three emended diagnoses were proposed for Chaetoceros vixvisibilis, Bacteriastrum jadranum and B. mediterraneum. The morphological analysis helped to clear previously common misidentifications of species Bacteriastrum delicatulum/B. furcatum, Chaetoceros contortus/C. compressus, C. decipiens/C. lorenzianus and C. lauderi/C. teres where that in all observed material only first species from the given pair could be identified. The individual morphological characters were classified according to their identification significance with the particular emphasis on comparison and establishing species-specific traits such as resting spore morphology, ultrastructure of the setae and valves. We distinguished 9 different setae structural types in the subgenus Chaetoceros and the same number in the subgenus Hyalochaete. A novel and unique type of colony formation in planktonic marine diatoms was discovered and characterized with the atomic force microscopy (AFM) for Bacteriastrum jadranum which forms colonies by enclosing the cells within the organic network (cell jacket). The phylogenetic analysis of 28S rDNA separated Bacteriastrum furcatum and B. hyalinum in one clade and B. jadranum and B. mediterraneum in the other one. In relation to other Chaetoceros species results imply that that Bacteriastrum species form a lineage within the genus Chaetoceros, but for the drastic changes in the taxonomy there is still a need for a more thorough investigation. The multivariate analysis of seasonal dynamics and ecological relationships showed the permanent presence of chaetocerotacean species in the phytoplankton with with a change in dominance and clear annual succession. The pattern can be partially explained by the environmental parameters, with the temperature, silicate, salinity and phosphate as most important factors driving the community succession.