Helitrons are newcomers among eukaryotic DNA transposons and have originally been identified by computational analysis in the genomes of Arabidopsis, rice and nematode. They are distinguished from other transposons in their structural features, and their proposed transposition mechanisms are involved in rolling circle replication. Computer-predicted autonomous Helitrons with conserved terminal sequences 5'-TC and CTRR-3' are presumed to encode a putative transposase, Rep/Hel-TPase, which contains a characteristic nuclease/ligase domain for the replication-initiation protein (Rep) and a DNA helicase domain (Hel). Plant Helitrons are thought to encode an additional transposase, RPA-TPase, which is related to the largest subunit of the replication protein A (RPA70). Although Helitrons are found in diverse genomes, neither an autonomous element nor a transposition event has been reported. Here we show that a spontaneous pearly-s mutant of Ipomoea tricolor cv. Pearly Gates, exhibiting white flowers and isolated in approximately 1940, has an 11.5-kbp novel Helitron, named Hel-It1, integrated into the DFR-B gene for anthocyanin pigmentation. Hel-It1 shows the predicted plant Helitron structure for an autonomous element with the conserved termini and carrying the two putative transposase genes, Rep/Hel-TPase and RPA-TPase, which contain a nonsense and a frameshift mutation, respectively. Hel-It1-related elements are scattered in the Ipomoea genome, and only a fraction of the pearly-s plants were found to carry Hel-It1 at another insertion site. The pearly-s mutant appears to bear an autonomous element and to express the wild-type RPA-TPase transcripts. The structures of a putative autonomous element and its transposase genes are discussed.