Marine photosynthetic microbial organisms are the major, sustaining components of ecosystem processes and are responsible for biogeochemical reactions that drive our climate changes. Despite this, many marine microorganisms are poorly described and little is known of broad spatial and temporal scale trends in their abundance and distribution. With new molecular and analytical techniques we can advance our knowledge of marine biodiversity at the species level to understand how marine biodiversity supports ecosystem structure, dynamics and resilience. We can then interpret environmental, ecological and evolutionary processes controlling and structuring marine ecosystem biodiversity. With better analytical methods available, we can augment our understanding of biodiversity and ecosystem dynamics in especially the pico- and nano-fractions of the plankton as well as in the deep sea benthos, both of which are very difficult to study. Here we provide examples of new and long standing molecular tools for researchers in marine ecosystems to enable them to provide better, faster and more accurate estimates of marine biodiversity in the community using tools at the forefront of molecular research.