A plant producing flowers with purple and white variegation was discovered in an accession of Glycine soja Siebold & Zucc. that was introduced from Russia. The mutant line was designated as B00146-m. Lines with white flowers (B00146-w) and purple flowers (B00146-r) were developed from the progeny of B00146-m. The flower color was controlled by the W1 locus encoding a flavonoid 3'5'-hydroxylase (F3'5'H). The allele for variegated flowers was designated as w1-m. The gene symbol was approved by the Soybean Genetics Committee. Polymerase chain reaction (PCR) suggested that a DNA fragment with a molecular size of similar to 3.9 kb was inserted in the first exon of the F3'5'H gene in B00146-m whereas such insertion was not observed in B00146-w and B00146-r. These results suggested that an active mobile element was inserted in the first exon and was responsible for flower variegation. The inserted fragment was identified as a 3883 bp long CACTA-family transposable element and it was designated as Tgs1. Similarity of overall sequence and terminal inverted repeats suggested that Tgs1 and the soybean lectin gene transposable element Tgm1 make up a subgroup. Frequency of germinal reversion was low probably due to the integration into an exon. Tgs1 had a truncated version of the transposase gene and may be a nonautonomous element.