Intracellular pH homeostasis is a prerequisite for biological processes and requires the action of proton pumps. The vacuolar H(+)-ATPase (V-ATPase) is involved in regulating pH in endomembrane compartments of all eukaryotic cells. In plants, there is an additional endomembrane proton pump, H(+)-pyrophosphatase (H(+)-PPase). However, the relative roles of the two types of pumps in endomembrane acidification and energization of secondary active transport are unclear. Here, we show that a strong T-DNA insertion allele of VHA-A, the single copy gene encoding the catalytic subunit of the Arabidopsis V-ATPase, causes complete male and partial female gametophytic lethality. Severe changes in the morphology of Golgi stacks and Golgi-derived vesicles in male gametophytes are the first visible symptoms of cell degeneration leading to a failure to develop mature pollen. Similar effects on Golgi morphology were observed in pollen tubes when growth was blocked by Concanamycin A, a specific V-ATPase inhibitor. Taken together, our results suggests that V-ATPase function is essential for Golgi organization and development of the male gametophyte.