We studied the effects of altitude, climate and hydrology on distribution of freshwater diatoms over the ecoregions of Israel. The previously recorded and recently revised taxonomic diversity of freshwater algae of Israel include 1621 species from which the diatoms constitute 32.3%. A notable feature of the taxonomic structure is a large proportion of monomorphic species with Index 1.09 ratio. Israel presents a unique diversity of algal environments from coastal plains to mountainous areas about 2000 m high and over four phytogeographic realms. Here we analyze statistical regularities of diatom distribution and compare them with the phytogeographic zonation based on higher plants. The 42 types of geographic ranges are combined in six phytogeographic domains. Five clusters of diatom taxa correspond to the coastal plains (I), the Judean and Galilean highlands (II), piedmonts (III), and the Dead Sea - Kinneret Lake Rift Valley (IV-V). Diatom flora contains both circumpolar and tropical species. The boundaries marked by the diatom distribution appear less distinct, with more numerous ecotonal species, than the corresponding terrestrial vegetation boundaries. Diatoms formed two floristic cores with centers in the Carmel and Judean mountains. The ten endemic diatoms are confined to the Rift Valley and adjacent areas of Central Negev. The differentiation of endemic species might  have occurred under the impact of aridization through the Holocene and the recent warming. Analysis shows that altitude is a major factor of diatom distribution in Israel.