Microbiome analysis of seawater samples collected at stations along Svalbard Cross Shelf transects, at different depths and replicated for three distinct sequencing strategies: V4-V5 16S rRNA gene, full-length 16S rRNA gene and Shotgun metagenomics). Samples were collected during the Norwegian Polar Institute MOSJ-ICE 2019 plankton-monitoring program. Samples were concentrated on board through Sterivex 0.2 mm filtration and preserved at -80ºC for later DNA extraction.The V4-V5 16S rRNA gene and Shotgun metagenomics was sequenced by Illumina and the full-length 16S rRNA gene was sequenced by PacBio CCS. This dataset will be expanded in the future, in order to have samples taken at the same geographic locations and with the same methodologies, during different years. Furthermore, this dataset is integrated with the MOSJ 2016 dataset, already made available (MGYS00003725)