The species distribution of heterotrophic flagellates has been investigated in accordance with the zonation of the White Sea silty-sandy intertidal flat. In Gryaznaya Bay of the Chernaya River Estuary (Kandalaksha Bay), 64 species and forms of flagellates have been identified. Three species (Ploeotia tenuis, Salpingoeca tuba, and Thecamonas trahens) are newly recorded for the White Sea. The species diversity, abundance, and biomass of heterotrophic flagellates were the highest in the upper and lower littoral horizons, as compared to the middle littoral and transitional zones. The species composition and community structure of heterotrophic flagellates depend on the local combinations of salinity and Eh rather than on the littoral zone and related sediments and the type and amount of organic material. The heterotrophic flagellate community within the intertidal zone has been subdivided into three groups: 1) species preferring biotopes of higher salinity at lower and upper boundaries of the mid intertidal zone, 2) species tending to silty sediments of the upper intertidal zone with lower salinity and Eh, and 3) species preferring the well-aerated slightly silted sands of the lower intertidal zone.