A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged with regard to the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. This investigation has evaluated microbial planktonic communities along a ~15,400 km Pacific Ocean transect with DNA from samples aquired every 2 degrees of latitude within a three month period between late August to early November, 2003. Next generation sequencing targeted Bacteria, Archaea, and Eukarya rDNA sequences.Beta analysis of ~10.8 million high quality sequences showed significant geographic patterns of microbial communities, primarily the Bacteria and Archaea domains. Despite regional clustering, none of the domains exhibited a unimodal pattern of alpha-diversity with respect to latitude. Bacteria communities increased in richness from Arctic to Antarctic waters whereas Archaea and Eukarya communities showed no latitudinal or polar trends. Based on these analyses, constraints on macrofaunal response to factors related to latitude may not be defining prokaryotic and eukaryotic microorganism diversity patterns in the global ocean.