Ascorbate peroxidase (APX) enzyme is an integral part of the plant tolerance response to environmental stresses. As a first step towards the study of the physiological role and the regulation of the members of the Apx gene family, the orthologs of the stress-sensitive cultivated tomato Solanum lycopersicum cv. M82 (Lem) and of the wild salt- tolerant species S. pennellii acc. Atico (Lpa) were identified by utilizing the tomato EST database, and characterized. The complete tomato Apx gene family is comprised of genes encoding three cytosolic, two peroxisomal, and two chloroplastic APXs. These genes attained differential regulatory patterns in various Lem and Lpa organs. More detailed study of Apx1 and Apx2 genes, that are the products of a recent gene duplication event, shows that they have already attained differential regulation within and between Lem and Lpa under control and stress conditions. It is also suggested that due to lineage-specific gene duplication and lose events, intricate phylogenetic relationships exist among the members of the Apx gene families.