ABSTRACT: Studies in several estuarine ecosystems along the mid-Atlantic coast of the USA were carried out to examine short-term (every 1 to 3 wk) to long-term (seasonal-annual) shifts in the phylotypic composition of the planktonic microbial eukaryotic assemblage using terminal restriction fragment length polymorphism (T-RFLP) analyses. Fragment patterns revealed relatively rapid and striking shifts in the dominant phylotypes observed. Although the presence of some phylotypes was persistent or repetitive, dramatic changes in the overall composition of the microbial eukaryotic assemblage were observed for samples collected from a single environment at 1 to 2 wk intervals, samples collected on the same day from neighboring locales, and samples collected from different seasons. Bray-Curtis similarity values rarely indicated ≥70% similarity for any 2 sample pairs. Non-metric multi-dimensional scaling and detrended correspondence analysis revealed a weak degree of relatedness among samples by location and season. Putative identifications of taxa comprising fragments of specific lengths were determined for 63 of the observed 162 fragment sizes from in silico restriction digests of partial 18S gene sequences obtained from the samples. This approach identified a wide phylogenetic diversity of protistan taxa, despite the presence of significant ‘brown tides’ caused by the pelagophyte Aureococcus anophagefferens at some sampling times and locations. The regularity and rapidity with which the protistan assemblage restructured itself to yield unique combinations of dominant taxa indicates the existence of a highly dynamic and resilient microbial community that responded swiftly to changing environmental conditions in these estuaries.