H(+)-translocating inorganic pyrophosphatases (H(+)-PPase) were recognized as the original energy donors in the development of plants. A large number of researchers have shown that H(+)-PPase could be an early-originated protein that participated in many important biochemical and physiological processes. In this study we cloned 14 novel sequences from 7 eremophytes: Sophora alopecuroid (Sa), Glycyrrhiza uralensis (Gu), Glycyrrhiza inflata (Gi), Suaeda salsa (Ss), Suaeda rigida (Sr), Halostachys caspica (Hc), and Karelinia caspia (Kc). These novel sequences included 6 ORFs and 8 fragments, and they were identified as H(+)-PPases based on the typical conserved domains. Besides the identified domains, sequence alignment showed that there still were two novel conserved motifs. A phylogenetic tree was constructed, including the 14 novel H(+)-PPase amino acid sequences and the other 34 identified H(+)-PPase protein sequences representing plants, algae, protozoans and bacteria. It was shown that these 48 H(+)-PPases were classified into two groups: type I and type II H(+)-PPase. The novel 14 eremophyte H(+)-PPases were classified into the type I H(+)-PPase. The 3D structures of these H(+)-PPase proteins were predicted, which suggested that all type I H(+)-PPases from higher plants and algae were homodimers, while other type I H(+)-PPases from bacteria and protozoans and all type II H(+)-PPases were monomers. The 3D structures of these novel H(+)-PPases were homodimers except for SaVP3, which was a monomer. This regular structure could provide important evidence for the evolutionary origin and study of the relationship between the structure and function among members of the H(+)-PPase family.