Marine organisms are the major, sustaining components of ecosystem processes and are responsible forbiogeochemical reactions that drive our climate changes. Despite this, many marine organisms are poorlydescribed 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 thespecies level to understand how marine biodiversity supports ecosystem structure, dynamics and resilience.We can then interpret environmental, ecological and evolutionary processes controlling and structuring marineecosystem biodiversity. With better analytical methods available, we can augment our understanding ofbiodiversity and ecosystem dynamics in especially the pico- and nano fractions of the plankton as well as in thedeep sea benthos , both of which are very difficult to study. We have provided examples of new and long standingmolecular tools for researchers in marine ecosystems to enable them to provide better, faster and more accurateestimates of marine biodiversity in the community using tools at the forefront of molecular research.