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Previously, a whole-genome comparison of three <i>Clostridium butyricum</i> type E strains from Italy and the United States with different <i>C. botulinum</i> type E strains indicated that the <i>bont</i>/<i>e</i> gene might be transferred between the two clostridia species through transposition. However, transposable elements (TEs) have never been identified close to the <i>bont</i>/<i>e</i> gene. Herein, we report the whole genome sequences for four neurotoxigenic <i>C. butyricum</i> type E strains that originated in China. An analysis of the obtained genome sequences revealed the presence of a novel putative TE upstream of the <i>bont</i>/<i>e</i> gene in the genome of all four strains. Two strains of environmental origin possessed an additional copy of the putative TE in their megaplasmid. Similar putative TEs were found in the megaplasmids and, less frequently, in the chromosomes of several <i>C. butyricum</i> strains, of which two were neurotoxigenic <i>C. butyricum</i> type E strains, and in the chromosome of a single <i>C. botulinum</i> type E strain. We speculate that the putative TE might potentially transpose the <i>bont</i>/<i>e</i> gene at the intracellular and inter-cellular levels. However, the occasional TE occurrence in the clostridia genomes might reflect rare transposition events.