Helical-shaped bacteria resembling Spirochaetes commonly are present in the gastrointestinal tract of animals and humans. Culturing of Spirochaetes is in general fastidious and not always successful. Here, a new DNA isolation approach for prokaryotic cells in formalin-fixed paraffin-embedded tissue samples is applied for the identification of an unknown Spirochaete. The tissue samples from colon were obtained from a previous study (1). Sectioning, in situ hybridization, LCM, DNA extraction, PCR reaction and sequencing were done according to Klitgaard et al. (2). The unknown invasive Spirochaetes species was recognized in pigs by using fluorescent in situ hybridization, followed by laser capture microdissection (LCM) of the targeted cells from the colonic mucosa. Direct 16S rRNA gene PCR was performed from the dissected micro-colonies. A phylogenetic analysis clustered the 16S rRNA gene in the Treponema genus group. The closest related Treponema type strain was T. bryantii (