Understanding the processes that shape the community structure of Arctic phytoplankton is crucial for predicting responses of Arctic ecosystems functioning to the ongoing ocean warming. In particular, little is known about the importance of phytoplankton dispersal by the North Atlantic current and the degree and maintenance of Arctic endemism. We investigated the diversity and biogeography of diatoms from five Svalbard fjords and from the observatory Hausgarten (Fram Strait) by combining algal isolation and cultivation and 18S rRNA gene metabarcoding. In total, 52 diatom strains were isolated from the area during the HE492 cruise in August 2017. The strains were taxonomically identified using molecular and morphological approaches, and their biogeographic distribution was mapped using the local metabarcoding dataset and a compilation of published metabarcoding datasets. Biogeographic analysis was also conducted for the locally most abundant diatom metabarcoding amplicon sequence variants (ASVs). The biogeographic analyses demonstrated that Arctic diatoms exhibit distinct biogeographic distribution patterns: Arctic-polar, Arctic-temperate, Arctic-cosmopolitan, temperate-cold and cosmopolitan. At Hausgarten and in Isfjorden the communities were dominated by genotypes with temperate-cold and cosmopolitan distribution, suggesting a strong influence of warmer Atlantic waters. Diatom communities in Van Mijenfjorden and Kongsfjorden were dominated by genotypes with broad, Arctic-temperate distribution and overall lower presence of temperate-cold species, indicating weaker Atlantic influence. The two northernmost fjords (Woodfjorden and Wijdefjorden) were dominated by species that appear biogeographically restricted to the Arctic realm. Our results demonstrate that the diatom community structure in the Svalbard area is shaped by an interplay of genotypes dispersed by warm Atlantic waters, genotypes restricted to the Arctic, and widely distributed genotypes, all of which are further structured by local environmental gradients. We suggest that warm-water diatom genotypes can be used as indicators of increased influence of Atlantic waters (i.e. “Atlantification”) on the plankton community structure in the Svalbard area.