Vacuolar H⁺-ATPase is a multisubunit protein complex, which fulfills a number of crucial functions in plant cells. Different mechanisms are known to be important for regulation of proton-transporting enzyme activity at the transcriptional and posttranslational levels. In this investigation we perform a comparison analysis of the molecular phylogeny of different subunits of vacuolar H⁺-ATPase directed in the elucidation of a conservative rate of membrane and peripheral complexes of the enzyme. High rate of conservatism was shown for subunits c, d and В, as well as ancient duplications of subunit a.