We evaluated the applicability of tRNA gene PCR in combination with fluorescent capillary electrophoresis with an ABI310 genetic analyzer (Applied Biosystems, Calif.) for the identification of different mollicute species. A total of 103 strains and DNA extracts of 30 different species belonging to the genera Acholeplasma, Mycoplasma, and Ureaplasma were studied. Reproducible peak profiles were generated for all samples, except for one M. genitalium isolate, the three M. gallisepticum isolates, and 8 of the 24 Ureaplasma cultures, where no amplification could be obtained. Clustering revealed numerous discrepancies compared to the identifications that had been previously obtained by means of biochemical and serological tests. Final identification was obtained by 16S rRNA gene amplification followed by sequence analysis and/or restriction digestion. This confirmed the identification obtained by tRNA gene PCR in all cases. Seven samples yielded an unexpected tRNA gene PCR profile. Sequence analysis of the 16S rRNA genes showed that six of these samples were mixed and that one had a unique sequence that did not match any of the published sequences, pointing to the existence of a not-yet-described species. In conclusion, we found tRNA gene PCR to be a rapid and discriminatory method to correctly identify a large collection of different species of the class of Mollicutes and to recognize not-yet-described groups.Having no cell wall, Mollicutes form a special class of bacteria. Their small, compact genomes evolved from AT-rich, gram-positive bacteria by means of genome reduction. At the same time, they developed innovative mechanisms to survive as parasitic organisms in a wide variety of host environments. To date, eight genera belonging to the class Mollicutes have been described, and within these genera, up to 200 species, mostly of the genus Mycoplasma, are acknowledged. This variety of species is associated with several taxonomic ambiguities (15,17,18), and a correct identification may be very difficult for numerous reasons. First, a number of Mollicutes, especially the plant-pathogenic spiroplasmas, have not been cultivated, while others require very complex media. As a result, for some species, only a limited number of isolates exist, and these are often not easily accessible. Second, as more sequences and better isolation media become available, more species are continuously being discovered. Finally, for some species, limited data and very few reports are published, especially for less-virulent and nonvirulent species.To correctly differentiate all these species, a universal and fast identification technique would be extremely useful. Some promising methods have already been described (see, e.g., reference 25), but they do not yield digitized data, making exchange between laboratories difficult. An optimized tRNA gene PCR technique, originally described by Welsh and McClelland (27,48), has been shown to be useful for correct and reproducible identification of very diverse bacterial species when combined with hig...