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Sporulation is a finely regulated morphogenetic program important in the ecology and epidemiology of <i>Clostridium botulinum</i>. Exogenous elements disrupting sporulation-associated genes contribute to sporulation regulation and introduce diversity in the generally conserved sporulation programs of endospore formers. We identified a novel prophage-like DNA segment, termed the <i>yin</i> element, inserted within <i>yabG</i>, encoding a sporulation-specific cysteine protease, in an environmental isolate of <i>C. botulinum</i>. Bioinformatic analysis revealed that the genetic structure of the <i>yin</i> element resembles previously reported mobile intervening elements associated with sporulation genes. Within a pure <i>C. botulinum</i> culture, we observed two subpopulations of cells with the <i>yin</i> element either integrated into the <i>yabG</i> locus or excised as a circular DNA molecule. The dynamics between the two observed conformations of the <i>yin</i> element was growth-phase dependent and likely mediated by recombination events. The <i>yin</i> element was not required for sporulation by <i>C. botulinum</i> but triggered an earlier entry into sporulation than in a related isolate lacking this element. So far, the <i>yin</i> element has not been found in any other <i>C. botulinum</i> strains or other endospore-forming species. It remains to be demonstrated what kind of competitive edge it provides for <i>C. botulinum</i> survival and persistence.