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During an oxidative stress-response assay on a putative Dps-like gene-disrupted &#916;<i>dgeo</i>_0257 mutant strain of radiation-resistant bacterium <i>Deinococcus geothermalis</i>, a non-pigmented colony was observed among the normal reddish color colonies. This non-pigmented mutant cell subsequently displayed higher sensitivity to H₂O₂. While carotenoid has a role in protecting as scavenger of reactive oxygen species the reddish wild-type strain from radiation and oxidative stresses, it is hypothesized that the carotenoid biosynthesis pathway has been disrupted in the mutant <i>D. geothermalis</i> cell. Here, we show that, in the non-pigmented mutant cell of interest, phytoene desaturase (Dgeo_0524, <i>crt</i>I), a key enzyme in carotenoid biosynthesis, was interrupted by transposition of an IS<i>Dge</i>7 family member insertion sequence (IS) element. RNA-Seq analysis between wild-type and &#916;<i>dgeo</i>_0257 mutant strains revealed that the expression level of IS<i>Dge</i>5 family transposases, but not IS<i>Dge</i>7 family members, were substantially up-regulated in the &#916;<i>dgeo</i>_0257 mutant strain. We revealed that the non-pigmented strain resulted from the genomic integration of IS<i>Dge</i>7 family member IS elements, which were also highly up-regulated, particularly following oxidative stress. The transposition path for both transposases is a replicative mode. When exposed to oxidative stress in the absence of the putative DNA binding protein Dgeo_0257, a reddish <i>D. geothermalis</i> strain became non-pigmented. This transformation was facilitated by transposition of an IS<i>Dge</i>7 family IS element into a gene encoding a key enzyme of carotenoid biosynthesis. Further, we present evidence of additional active transposition by the IS<i>Dge</i>5 family IS elements, a gene that was up-regulated during the stationary phase regardless of the presence of oxidative stress.