The family of Ser/Thr and/or Tyr kinases and that of His kinases play essential roles in signal transduction. For a long time, the former has been found in eukaryotes, the latter in prokaryotes. Studies in the last decade have shown, however, that most bacteria possess from one to more than 10 genes encoding Ser/Thr kinases. This observation raises an important question concerning the evolutionary origin of Ser/Thr kinases found in bacteria. To answer this question, we have analyzed a family of 11 genes encoding Ser/Thr kinases in the cyanobacterium Synechocystis sp. PCC 6803. This bacterium contains the largest number of Ser/Thr kinases among all bacteria whose genomic sequences have been released so far. In this study, we have developed a user-friendly computer program for statistical analysis of codon usages and GC content. The results demonstrate that Ser/Thr kinases have similar codon usages and GC contents as the average of all possible open reading frames (ORFs) deduced from the genome. In contrast, ORFs encoding transposases, as a control in our analysis, display a disparity in both codon usage and GC content, confirming their multiple origin and genetic promiscuity. In light of our results, we propose that Ser/Thr kinases existed before the divergence between prokaryotes and eukaryotes during evolution, or were laterally transferred into prokaryotes at the early stages of bacterial evolution. If Ser/Thr kinases have persisted ever since in prokaryotes under evolutionary pressure, it is then expected that they play important, possibly even essential roles in regulating bacterial activities as do their counterparts in eukaryotes.