Marine microbial biogeography describes the occurrence and abundance of microbial taxa and aims to understand the mechanisms by which they are dispersed and then adapt to their environment. The development of novel technologies, such as Next-Generation Sequencing (NGS) in combination with large-scale ocean sampling campaigns, generated a vast amount of taxonomic data that allowed for in-depth analyses of biogeographic patterns. Globally occurring groups of microorganisms were detected that dominate the marine environment (e.g., SAR11, SAR86, Roseobacter, and Vibrio), however, NGS data revealed the presence of distinct eco- and phylotypes inside these clades and genera that showed clear ecological niche adaptation and different biogeographic distributions. Genome analyses of these marine microorganisms helped to understand potential adaptive mechanisms that could explain why certain taxa are occurring ubiquitously and others are limited to certain regions and ecosystems. Marine microorganisms can employ a vast variety of adaptive mechanisms to deal with environmental parameters such as temperature, light or nutrient availability, for example through exploitation of specific energy sources or protective mechanisms against UV radiation or viruses. The availability or lack of physiological pathways and traits in ecotypes is then responsible for shaping the marine microbial biogeography.