The work aims the study the species diversity and ecology of Cyanobacteria in the benthos on the Israeli coast of the Mediterranean Sea. As a result, 24 taxa of Cyanobacteria were found. Seven taxa were noted for the first time for this sea: Aphanocapsa incerta, Aphanothece nidulans, Chlorogloea cf. microcystoides, Pseudanabaena mucicola, Chroococcus sp., Gloeocapsopsis sp., Trichocoleus sp. Most Cyanobacteria species were benthic (90 %) and marine (67 %). There were only four indicators of saprobity, and all of them were freshwater species common in oligosaprobic and beta-mesosaprobic waters. Most species had a wide geographic distribution. Species marked of boreal (10 %), boreal-tropical (38 %), arctic-boreal-tropic (29 %) and cosmopolites (24 %) groups. The species richness of Cyanobacteria increased in the sites with the maximal anthropogenic loads from industrial and urban areas of the central Israel, and the minimal ones were in the protected areas.