Marine biodiversity scientists aim to catalogue the Oceans entire species in the framework of the Census of the Marine Life (CoML). The goal of attaining a complete understanding the roles and interactions of these species, both in terms of the natural and human economies of the planet, is the final goal.
Others obstacles have more to do with the sociology of science than the science itself. High tech routinely trumps basic natural history, and people who know how to identify and classify organisms are almost as endangered as many of the creatures they study. We have been slow to appreciate this for ocean life. Turtles hover on the brink of extinction, yet we only now are beginning to know where they go once they leave the beach. Coral reefs have declined dramatically over the last two decades worldwide, but our only estimates for the total number of species on reefs vary between one and ten million and are based on extrapolations from the numbers of insects in tropical rainforests and from counts from a tropical aquarium in Baltimore. Ongoing attempts to create a database for all of the oceans as the Census for Marine Life are playing an essential role in filling the knowledge gaps that plague our ability to document and cope with the threats to ocean life, but they are just beginning. The limited knowledge of species diversity in many areas of the globe, coupled with anthropogenic disturbance of ecosystems, has prompted calls for an improved system of inventorying biodiversity and disseminating taxonomic information.
DNA barcoding works very well in varied marine systems, but researchers must be prepared for substantial increase in species numbers. A well functioning program for barcoding marine organisms based on large-scale analytical capacity would have far-reaching scientific advantages. Thus, DNA barcoding of marine species will help substantially to address the second grand challenge of the Census of Marine Life (CoML), “What lives in the ocean now?”
Further information on the possible extend of the challenge you'll find in
Philippe Bouchet "The magnitude of marine biodiversity."
in Carlos Duarte (ed.), "The Exploration of Marine Biodiversity", Fundacion BBVA, Bilbao, 2006, pp. 31-62.