The plant vacuolar H(+)-translocating ATPase (V-ATPase, EC 3.6.1.34) generates a H+ electro-chemical gradient across the tonoplast membrane. We isolated two full-length cDNA clones (VHA-A1 and VHA-A2) from tomato (Lycopersicon esculentum Mill. cv. Large Cherry Red) coding for two isoforms of the V-ATPase catalytic subunit (V-ATPases A1 and A2). The cDNA clones encoding the two isoforms share 90% identity at the nucleotide level and 96% identity at the amino acid level. The 5'- and 3'-untranslated regions, however, are highly diverse. Both V-ATPase A1 and A2 isoforms encode polypeptides of 623 amino acids, with calculated molecular masses of 68,570 and 68,715, respectively. The expression of VHA-A1 and accumulation of V-ATPase A1 polypeptide were ubiquitous in all tissues examined. In response to salinity, the abundances of both transcript (VHA-A1) and protein (V-ATPase A1) of the A1 isoform in leaves were nearly doubled. In contrast to the A1 isoform, VHA-A2 transcript and V-ATPase A2 polypeptide were only detected in abundance in roots, and in minor quantities in mature fruit. In roots, accumulation of transcripts and polypeptides did not change in response to salinity for either isoform. Subcellular localization indicated that the highest levels of both V-ATPase A1 and A2 isoforms were in the tonoplast. However, significant quantities of both isoforms were detected in membranes associated with endoplasmic reticulum and/or Golgi. Immunoprecipitation of dissociated V1 domains using isoform-specific antibodies showed that V1 domains consist of either V-ATPase A1 or A2 catalytic subunit isoforms.