ABSTRACT: Our understanding of biodiversity patterns within the world’s oceans is limited and primarily based on coastal communities and specific taxa. Furthermore, the assessment of global biodiversity often relies on disparate methodologies, which can bias the findings. This is particularly true for many metazoan taxa whose diversity across the oceans remain relatively unknown. Metabarcoding of environmental DNA can assess the diversity of organisms throughout the entire metazoan subkingdom, and allow a much greater spatial coverage and quantity of samples compared to traditional surveys, which are often cost-limited and labor intensive. We utilized large genomic databases from two separate cruises that circumnavigated the Earth and sampled from the ocean’s surface down to 4000 meters to assess what factors affect the diversity of metazoans. Results indicate different patterns for separate phylums of metazoans that are associated with temperature, depth and latitude. Environmental DNA offers an unprecedented way to measure marine diversity and determine factors that affect communities on the surface and into the deep oceans. Determining global patterns of diversity within our oceans is of the utmost importance given the current, unprecedented rates of change occurring within marine ecosystems.