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Since March 1986, there has been a monthly time series collected through water sampling in the Gulf of Trieste. The sampling station (C1-LTER, 45º42'30"N 13º42'36"E) is located 200 m from the coastline with a water depth of 18 m. Water-column samples (0.5, 5, 10, and 15 m) were analyzed from the 1986-2010 time series (Cabrini et al., 2012) in order to identify phytoplankton seasonal evolution and community structure. The analysis of total phytoplankton composition showed a clear seasonal cycle with peak concentration values in late winter to early spring due to monospecific diatom blooms, and low values in late spring to summer when the phytoplankton is dominated by small flagellates. There is a second smaller peak in the fall that is dominated by diatoms, and low values occur in early winter, when nanoflagellates dominate. In addition, Cabrini et al. (2012) detected an important regime shift within the analyzed time series: a period from 1986 to 1994 that is characterized by high phytoplankton abundance values and dominated by phytoflagellates, and a second period from 1995 to 2007 with low cell concentrations that is dominated by diatoms. In this work, we analyzed the time series from August 2011 to July 2012, specifically addressing the vertical and seasonal distribution of selected phytoplankton groups – those possessing a mineralized skeleton and thus potentially preserved in the sediments and able to leave a fossil record. Coccolithophores are a major group in the oligotrophic eastern Mediterranean, and Cabrini et al. (2012) showed that they also can be seasonally important in the shallow areas of the Gulf of Trieste. In the present dataset, coccolithophores showed a primary abundance peak (up to 3.2x105 coccospheres/liter) from November to February and a second smaller peak (up to 1x105 coccospheres/ liter) in May to June. Emiliania huxleyi was the most abundant species throughout the analyzed time series, but Acanthoica quattrospina also made an important contribution in January, while holococcolithophores (A. quattrospina HOL, Corisphaera gracilis, C. strigilis, and C. mediterranea HOL) and small Syracosphaera species were the most important group within the May to June peak. In addition, there was a widespread occurrence, especially in the subsurface layer, of species inhabiting the intermediate photic zone during the late summer to fall period (Algirosphaera robusta, Calciopappus rigidus, Ophiaster hydroideus, and Calciosolenia spp.), while Rhabdosphaera clavigera and Syracosphaera pulchra were most important during the summer months. Among the flagellate groups, Cabrini et al. (2012) reported silicoflagellates and ebridians from the Gulf of Trieste. Worldwide, these silicifying groups make a minor contribution to phytoplankton, and little is known about their specific vertical and seasonal distribution because only a few studies have dealt with their occurrence in water samples. An improved knowledge of their ecological characteristics would be of great value, considering their potential use in paleoecological reconstructions. In the present dataset, the occurrence of silicoflagellates was restricted to the fall-winter-spring period. Octactis pulchra was the dominant species, occurring throughout the water column from September to March, with peak values (8x104 cells/liter) in January. Dictyocha species were present from September to January, primarily in the subsurface layers, while Distephanus speculum occurred only sporadically at different times and depths. Ebridians also showed a very clear seasonality, with Ebria tripartita occurring from January to March in the sub-surface layers and Hermesinum adriaticum occurring throughout the water column from June to August.