Horizontal gene transfer (HGT) is a significant process in prokaryotic genome evolution, with operational genes (involved in housekeeping functions) being more frequently transferred than informational genes (involved in transcription, translation, and related processes). This study analyzed six complete prokaryotic genomes and identified 312 orthologous gene sets to test two hypotheses about HGT: the continual transfer hypothesis and the early massive transfer hypothesis. The results support the continual transfer hypothesis, showing that operational genes have been continuously transferred since the divergence of prokaryotes, rather than in a few massive events early in their evolution. The complexity hypothesis is proposed to explain this difference: informational genes are part of complex systems, making their horizontal transfer less likely compared to operational genes, which are part of simpler systems. The study also found that the evolutionary rates of operational and informational genes are similar, suggesting that factors other than rate of evolution influence HGT. Phylogenetic analyses and distance metrics confirmed that operational genes experience more horizontal transfers than informational genes, supporting the continual transfer hypothesis. The complexity of informational genes likely restricts their successful horizontal transfer, while operational genes are more likely to be transferred due to their simpler structure. The study highlights the importance of HGT in prokaryotic genome evolution and suggests that operational genes play a more significant role in this process.Horizontal gene transfer (HGT) is a significant process in prokaryotic genome evolution, with operational genes (involved in housekeeping functions) being more frequently transferred than informational genes (involved in transcription, translation, and related processes). This study analyzed six complete prokaryotic genomes and identified 312 orthologous gene sets to test two hypotheses about HGT: the continual transfer hypothesis and the early massive transfer hypothesis. The results support the continual transfer hypothesis, showing that operational genes have been continuously transferred since the divergence of prokaryotes, rather than in a few massive events early in their evolution. The complexity hypothesis is proposed to explain this difference: informational genes are part of complex systems, making their horizontal transfer less likely compared to operational genes, which are part of simpler systems. The study also found that the evolutionary rates of operational and informational genes are similar, suggesting that factors other than rate of evolution influence HGT. Phylogenetic analyses and distance metrics confirmed that operational genes experience more horizontal transfers than informational genes, supporting the continual transfer hypothesis. The complexity of informational genes likely restricts their successful horizontal transfer, while operational genes are more likely to be transferred due to their simpler structure. The study highlights the importance of HGT in prokaryotic genome evolution and suggests that operational genes play a more significant role in this process.