Phytoplankton have traditionally been identified based on morphological characteristics. However, identifications based on morphology are time-consuming, require expertise in taxonomy, and often fail to distinguish differences among the multitudes of minute, nondescript planktonic organisms. Molecular techniques, which have revealed new insights into bacterial and picoplankton communities, may also enhance our knowledge of the diversity among communities of larger plankton. We compared plankton identifications and community assessments based on the two types of techniques (morphological vs molecular) for surface seawater samples collected on 2 May, 31 July and 25 September 2000 from several sampling stations in the Bay of Fundy. Phytoplankton captured in surface bucket samples were quantified and identified based on morphology. DNA was extracted from plankton communities (5–100 μm in diameter) collected by filtration, and 18S rRNA gene fragments were amplified with primers specific for eukaryotes. Denaturing gradient gel electrophoresis (DGGE) was used to develop DNA profiles of eukaryotic phylogenetic diversity and to select cloned 18S rDNA fragments for sequencing. Both morphological and molecular methods showed great community diversity. However, the communities identified with the two different types of techniques were starkly different. Morphological abundances and taxon richness were lowest in the May samples, whereas the number of DGGE bands was highest in May and July. Morphological identifications showed a succession of dominant organisms through time. Whereas neither diatoms nor dinoflagellates were dominant in May, diatoms and a few dinoflagellates were dominant in July and September. In contrast, few 18S rDNA sequences were related to rDNA sequences of known identity, and furthermore, few diatoms were identified in the molecular analyses. Molecular phylogenetic analysis indicated the presence of many novel organisms, several of which were most closely related to other unidentified sequences from diverse marine environments representing new lineages. Our results support the ideas that we are just beginning to uncover the diversity of eukaryotic marine organisms and that there may be many more ubiquitous, microeukaryotic plankton than previously realized. Our results suggest that both types of methods capture only a portion of the community. Morphological methods may be more adept at capturing the phototrophic organisms within the community. However, just as for bacteria and picoplankton, molecular techniques can enhance our understanding of plankton diversity, particularly by detecting previously unidentified organisms.