Five different DNA insertions (ISH1, ISH2, ISH23, ISH24, and ISH25) are found in or upstream of the bacterio-opsin (bop) gene in Bop mutants of H. halobium. These insertions have been cloned and characterized. They range in size from 520–3,000 bp, and four of the five insertions have structural features similar to known transposable elements. Two of the elements (ISH1 and ISH2) are found in the majority of Bop mutants. The former integrates at a preferred target site, while the latter integrates at numerous sites. The copy number of each insertion element was determined along with its distribution in the 68% G+C (FI), 58% G+C (FII) and cccDNA fractions of the H. halobium genome. There are eight copies of ISH2, one copy in FI and seven in the cccDNA. There are two copies of each of the other three insertion elements and one copy of ISH25. ISH25 does not seem to have the usual structural features of a transposable element. Most of the copies of these insertion elements are located in the cccDNA. Vacuole, ruberin and purple membrane mutants of H. halobium occur at high spontaneous frequencies. Rearrangements, insertions and deletions occur concurrently in the FII and cccDNA of these mutants including insertions of these five elements. Although the bacterio-opsin gene incurs insertions frequently, the 40 kb of flanking FI DNA remains conserved in mutant derivatives of H. halobium and in a number of related species.