The phylogenetic diversity of two continental shelf picoplankton communities was examined by analyzing SSU (16S) ribosomal RNA (rRNA) genes amplified from environmental DNA with bacterial-specific primers and the polymerase chain reaction (PCR). Picoplankton populations collected from the pycnocline (10 m) over the eastern continental shelf of the United States near Cape Hatteras, North Carolina, and surface seawater (10 m) from the western continental shelf of the United States 8 km west of Yaquina Head, Oregon, served as sources of bulk nucleic acids used in this study. A total of 285 SSU rRNA gene clones were analyzed in the two libraries, more than doubling the number previously available from seawater samples. In contrast to previous studies of bacterioplankton diversity from the open-ocean, a large proportion of the rDNA clones recovered in this study (38%) were related to plastid SSU rRNA genes, including plastids from bacillariophyte, prymnesiophyte, cryptophyte, chrysophyte, and prasinophyte algae, as well as a number of unique plastid rRNA gene clones for which no close phylogenetic relatives were discovered. A majority of the bacterial gene clones recovered (72% of bacterial clones) were closely related to rRNA gene lineages discovered previously in clone libraries from open-ocean marine habitats, including the SAR86 cluster (�� Proteobacteria), SAR83, SAR11, and SAR116 clusters (all �� Proteobacteria), the marine Gram-positive cluster (Actinomycetes), the marine group A/SAR406 cluster, and a cluster of environmental clones within the flexibacter-cytophaga-bacteroides phylum. A majority of the remaining bacterial clones were phylogenetically related to the �� and �� subclasses of the Proteobacteria, including an rDNA lineage within the Type I methylotroph Glade of the �� subclass. The abundance of plastid rDNAs and the lack of cyanobacterial-related clones, as well as the presence of �� Proteobacteria, are features of these coastal picoplankton gene clone libraries which distinguish them from similar studies of oligotrophic open-ocean sites. Overall, however, these data indicate that a limited number of as yet uncultured bacterioplankton lineages, related to those previously observed in the open-ocean, can account for the majority of cells in these coastal marine bacterioplankton assemblages. / Graduation date: 1998