text: Because T-RFLP relies on DNA extraction methods and PCR, the biases inherent to both will affect the results of the analysis. Also, the fact that only the terminal fragments are being read means that any two distinct sequences which share a terminal restriction site will result in one peak only on the electropherogram and will be indistinguishable. Indeed, when T-RFLP is applied on a complex microbial community the result is often a compression of the total diversity to normally 20-50 distinct peaks only representing each an unknown number of distinct sequences. Although this phenomenon makes the T-RFLP results easier to handle, it naturally introduces biases and oversimplification of the real diversity. Attempts to minimize (but not overcome) this problem are often done by applying several restriction enzymes and/ or labeling both primers with a different fluorescent dye. The inability to retrieve sequences from T-RFLP often leads to the need to construct and analyze one or more clone libraries in parallel to the T-RFLP analysis which adds to the effort and complicates analysis. The possible appearance of false (pseudo) T-RFs, as discussed above, is yet another drawback. To handle this researchers often only consider peaks which can be affiliated to sequences in a clone library.