The regulation of pH in cellular compartments is crucial for intracellular trafficking of vesicles and proteins and the transport of small molecules, including hormones. In endomembrane compartments, pH is regulated by vacuolar H(+)-ATPase (V-ATPase), which, in plants, act together with H(+)-pyrophosphatases (PPase), whereas distinct P-type H(+)-ATPases in the cell membrane control the pH in the cytoplasm and energize the plasma membrane. Flower colour mutants have proved useful in identifying genes controlling the pH of vacuoles where anthocyanin pigments accumulate. Here we show that PH5 of petunia encodes a P(3A)-ATPase proton pump that, unlike other P-type H(+)-ATPases, resides in the vacuolar membrane. Mutation of PH5 reduces vacuolar acidification in petals, resulting in a blue flower colour and abolishes the accumulation of proanthocyanidins (condensed tannins) in seeds. Expression of PH5 is directly activated by transcription regulators of the anthocyanin pathway, in conjunction with PH3 and PH4. Thus, flower coloration, a key-factor in plant reproduction, involves the coordinated activation of pigment synthesis and a specific pathway for vacuolar acidification.