Selenomonas ruminantium is a predominant lactate utilizing rumen bacterium and it could be considered a candidate organism for strain development through recombinant DNA technology. However, progress towards understanding the genetic organization of this species has been limited by the absence of a generalized method for transformation and the poor insight into S. ruminantium plasmid biology. Up to now, nine small cryptic plasmids has been characterized from this species. Five of them are rolling circle replicating plasmids belonging to the RepL family of plasmids; the others do not fall to any well defined plasmid family. Comparative genomic analysis has revealed striking similarities in RepL S. ruminantium plasmid genetic organization. While Rep proteins are only distantly related, small parts of the plasmid non-coding sequences were conserved at 80-90% identity among the different plasmids. All conserved sequence regions were found downstream rep genes. Although only limited sequence conservation was detected upstream of rep, this region was found to exhibit a significant secondary structure and participates probably in plasmid replication initiation.