Signal transduction is vitally important for development and cell survival of all animals. Most of signaling processes involve phosphorylation and dephosphorylation of amino acid residues in proteins. The kinases and phosphatases involved in signaling processes are regulated by different mechanisms. So far, the studies on protein phosphorylation almost exclusively limited to protein serine/threonine and tyrosine phosphorylation, phosphorylation of histidine has only been sparsely reported. However, phosphorylation of histidine residues has been extensively studied in prokaryotes. It is estimated that histidine phosphorylation may account for 6% of total protein phosphorylation in eukaryotes, 10- to-100-fold more than phosphotyrosine, though less abundant than phosphoserine. Although the presence of phosphohistidine in vertebrate protein was described as early as in the 1960s, accumulated knowledge in vertebrates so far is still limited to O-phosphates. The protein phosphatases were introduced, and the knowledge on the key mechanisms of the bacterial two-component system was summarized. Most importantly, novel mechanisms of phosphorylation and dephosphorylation of histidine residues are described. Finally, the recent studies about histidine phosphatases are discussed.