The original check-list of benthic microalgae of the Black Sea is proposed. The 1007 described taxa are Bacillariophyta, Cyanoprocaryota, Dinophyta, Chlorophyta, Chrysophyta, Euglenophyta, and Cryptophyta (832, 110, 24, 23, 10, 6 and 2, respectively). For the first time 91 species, varieties and forms, 67 genera are listed, among them 22 genera and 74 taxa formerly unknown in the Black Sea; taxonomic status of 25 diatoms was amended. 373 taxa from different localities were registered, including coastal sea water of the Caucasus and the Crimea, and Zernov's Phyllophora field (ZPF): 103/53 genera, 318/127 and 156/62, respectively. Taxonomic structure of microphytobenthos in the regions consists of 7 divisions, which are Bacillariophyta, Cyanoprocaryota, Dinophyta, Chlorophyta, Chrysophyta, Euglenophyta, and Cryptophyta (305, 21, 16, 18, 6, 5, and 2, respectively). The spring peak of density, biomass of development of microphytobenthos of the Black sea is set. For the first time production parameters of microphytobenthos on hard substrata were investigated. Annual production was estimated 300 g C·m-2 during a year. The microphytobenthos maintain biotic balance positive (1,79-8,3) year round, with largest estimates falling on April - October. Microphytobenthos and phytoplankton are members of a single ecofloristic microalgal complex that inhabits coastal seawater zone. The two ecotopes harbor 184 taxa, 132 are microphytobenthos, 86 phytoplankton and 33 species are common to both. Phytoplankton sedimentation entails species differentiation by biotopes in the microalgal community structure: floristic similarity index yields largest estimates in summer, when phytoplankton is settling onto the sea floor, and smallest in spring under mass growth of sedentary benthic diatoms (Ks=0,38 and Ks=0,14, respectively). The percentage of benthic and benthoplankton species in phytoplankton like that of plankton species in microphytobenthos equals 10-20%. It was found that microphytobenthos develops a peak in spring, and phytoplankton has spring peak of abundance and summer peak of biomass; Shannon index values were highest in spring microphytobenthos and in summer phytoplankton (H=4,25 and H=4,26, respectively). During a year (20-60 µm) diatoms predominate in the size structure of microphytobenthos, and (20-100 µm) diatoms and dinoflagellates in the phytoplankton. For the first time the inventory of potentially harmful microalgae was taken for the Black Sea and the Sea of Azov and the atlas prepared with the description of 79 species, their ecology, phytogeography and toxicity characteristics. 76 species were found in the Black Sea, half of them in benthos. Pseudo-nitzschia calliantha, the domoic acid-producing diatom new in the Black Sea, was found in the coastal sea water of the Crimea. Toxin concentration in the culture of Black Sea clone varied from 0,08 to 1,3 pg/cell.