Marine diatoms (Bacillariophyceae) are siliceous, single celled eukaryotes, important primary producers on a global scale and very diverse. Their taxonomic composition is driven by environmental conditions, thus, diatoms are frequently used as indicators for paleoenvironmental reconstructions. Here, we used sedimentary ancient DNA metabarcoding and investigated taxonomic diversity and composition along two marine sediment cores, one from Eastern Fram Strait, dating back to 29 kyr BP (N 78.915662, E 6.767167) and one from the North Pacific Ocean dating back 18 kyr BP (N 53.992660, E 162.375830). We amplified a 76 bp diatom-specific barcode of the rbcL gene. Among 9,356,222 assigned sequences, all four classes of diatoms are represented. Sequence types from polar centric diatoms dominate both datasets with most abundant sequence types assigned to the genera <em>Thalassiosira</em>, <em>Chaetoceros</em> and <em>Porosira</em>. In Eastern Fram Strait, taxonomic richness is slightly higher in samples ranging from the last glacial until its terminal stage than in samples from the period of the Bølling-Allerød to the late Holocene. In contrast, the Holocene samples of the North Pacific core show a slightly higher taxonomic richness than the pre-Holocene ones. In this study we demonstrate that ancient DNA metabarcoding of diatoms has the potential to assist and complement the analysis of long-term developments of community composition and diversity, e.g. in areas of low diatom preservation due to silica dissolution. Beyond that, it has promise in the investigations of genetic relationships, microevolution and population structure, which cannot be achieved in such detail using morphological remains.