Despite their small size, viruses have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. Due the high abundance of their hosts, bacteriophages or phages comprise the majority of viruses and provide the largest reservoirs of unexplored genetic diversity in marine environments. The rise of Next Generation Sequencing (NGS) techniques brings new opportunities to investigate the marine virus community. However, there is no current statutory pipeline applied in marine phage ecology. Therefore, this thesis proposes a virus-specific pipeline based on the integration of existing tools and state of the art techniques. The developed pipeline was applied to accomplish the two research aims of this thesis: (1) to analyze the virus community in the North Sea with viromics(virus metagenomics), and (2) to characterize lysogenic phages from potentially pathogenic Vibrio species. The results of the first part of this thesis show that the virus community is dominated by phages and they are not evenly distributed throughout the North Sea. In general, the coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. In the second part, lysogenic Vibrio phages from the North Sea were induced (ca. 40 % of tested isolates) and four phage genomes were characterized. The phages from V. parahaemolyticus (2 tailed phages, 1 filamentous phage) and V. cholerae (1 tailed phage) can integrate into their host genome and might have a role in pathogenicity. This thesis represents an exemplary study of the virus community in the North Sea, with special emphasis on the marine phages. The settled virus-specific pipeline the obtained insights will contribute to extend the study of the virus diversity dynamics in other marine areas to characterize novel phage groups.