Iceland is at the center of a contrasting hydrography, with cold Arctic water coming in from the north and warmer Atlantic water from the south. Phytoplankton play a crucial role in the marine food web and are sensitive indicators of environmental change, yet little is known of their diversity and distribution in this area of accelerated climate change. DNA metabarcoding can help expose the biogeography of phytoplankton in relation to oceanographic parameters by providing high resolution information on microbial diversity and distribution, particularly the diversity of cryptic and small species that are often not detected by microscopy. Seawater samples were collected in spring (2012 to 2018), summer (2017) and winter (2018) and together with corresponding physico-chemical metadata around Iceland. Amplicon sequencing of the V4 region of the 18S rRNA gene indicates that eukaryotic phytoplankton community composition is different between the northern and southern water masses, with some genera completely absent from Polar Water masses. Emiliana was more dominant in the Atlantic-influenced waters and in summer, and Phaeocystis was more dominant the colder, northern waters and in winter. Nano- and picophytoplankton taxa were more abundant and diverse than previously estimated based on microscopic surveys, with certain Chlorophyta genera similarly dominant to key diatom genera such as Chaetoceros.This study presents an extensive dataset for further investigation into the microdiversity and biogeography of marine protists around Iceland.