Several endogenous transposable elements such as Tgm1, Tgm2, Tgm3, Tgm4, Tgm5, Tgm6, Tgm7, Tgm8, Tgm9, Tgmt* and TgmR* have been identified in soybean [14, 38–40]. Of these, Tgm9 has been shown to be active and has recently been used to clone a male-sterile, female-sterile gene (GmMER3) that encodes an ATP dependent DNA helicase [14, 41, 42]. It is possible, although unlikely, to have another Tgm sequence(s) causing mutation in GmMER3 or other genes investigated in this study. To determine if the mutation in the male-sterile, female-sterile (mer3) mutant was caused by Tgm9, and not by any other active elements such as Tgmt*, the 3’-end 2,523 bp region of the transposon in the GmMER3 gene of the mer3 mutant was amplified and sequenced. The sequence matched perfectly with the Tgm9 sequence suggesting that the mer3 mutation was caused by Tgm9 insertion, not by Tgmt* (S4 Fig). Furthermore, sequencing of the T322 genome revealed that Tgm9 is the only intact CACTA-type element identified in this cultivar. In addition to the expected location of Tgm9 in W4, an additional copy of the element was identified in a locus on Chromosome 19. This Tgm9 element was hemizygous in T322 and absent among 15 selected Tgm9-induced mutants. This suggests that most likely the Tgm9 copy on Chromosome 19 was generated from a recent transposition event (J. Baumbach, S. Srivastava and M.K. Bhattacharya, unpublished).