A combined sequence-based and fragment-based characterization of microbial eukaryote assemblages provides taxonomic context for the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method

► We compared sequence- and fragment-based characterizations of microbial eukaryotes. ► Sequence information provided taxonomic context for the T-RFLP method. ► Fragments generally represented dominant sequence-based operational taxonomic units. ► T-RFLP was useful for the rapid analysis and comparison of microbial eukaryotes.