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DNA sequence polymorphisms display different migration profiles from wild-type fragment patterns when DNA is digested with restriction fragments and separated by size. T-RFLP (terminal-RFLP) analysis is a culture-independent RFLP method (only terminal fragments are labeled and detected) used to study highly complex microbial populations, based on variations in 16S rRNA (ribosomal RNA). This technique allows researchers to examine complex communities without the need for any genomic sequence information. This method is rapid, sensitive, reproducible, and enables the study of bacterial populations in diverse natural habitats, and the organisms’ responses to changes in environmental or physiological parameters.<br />DNA fragment analysis enables a multitude of applications from genotyping to bacteria identification and from plant screening to gene expression profiling.