Toxin-antitoxin (TA) loci are highly abundant in free-living prokaryotes but are absent in host-associated organisms. This study analyzed 126 completely sequenced prokaryotic genomes (16 archaea and 110 bacteria) and identified 671 TA loci belonging to seven known TA gene families. Free-living, slowly growing prokaryotes, such as Mycobacterium tuberculosis and Nitrosomonas europaea, had many TA loci, while obligate intracellular organisms had none. TA loci were often clustered and closely linked to mobile genetic elements. In Vibrio cholerae, all 13 TA loci were located within a mega-integron, suggesting they are mobile cassettes that move frequently. These findings support the hypothesis that TA loci function as stress-response elements beneficial to free-living prokaryotes. TA loci are involved in quality control of gene expression, particularly under stress conditions. The study also highlights the importance of TA loci in free-living organisms, where they may help maintain cellular stability and survival under unfavorable conditions. In contrast, host-associated organisms do not retain TA loci, possibly because they do not experience the same stress conditions. The presence of TA loci in free-living organisms suggests that they play a crucial role in their survival and adaptation to changing environments. The results indicate that TA loci are mobile elements that can be transferred between chromosomes and may contribute to the evolution of prokaryotic genomes.Toxin-antitoxin (TA) loci are highly abundant in free-living prokaryotes but are absent in host-associated organisms. This study analyzed 126 completely sequenced prokaryotic genomes (16 archaea and 110 bacteria) and identified 671 TA loci belonging to seven known TA gene families. Free-living, slowly growing prokaryotes, such as Mycobacterium tuberculosis and Nitrosomonas europaea, had many TA loci, while obligate intracellular organisms had none. TA loci were often clustered and closely linked to mobile genetic elements. In Vibrio cholerae, all 13 TA loci were located within a mega-integron, suggesting they are mobile cassettes that move frequently. These findings support the hypothesis that TA loci function as stress-response elements beneficial to free-living prokaryotes. TA loci are involved in quality control of gene expression, particularly under stress conditions. The study also highlights the importance of TA loci in free-living organisms, where they may help maintain cellular stability and survival under unfavorable conditions. In contrast, host-associated organisms do not retain TA loci, possibly because they do not experience the same stress conditions. The presence of TA loci in free-living organisms suggests that they play a crucial role in their survival and adaptation to changing environments. The results indicate that TA loci are mobile elements that can be transferred between chromosomes and may contribute to the evolution of prokaryotic genomes.