The phytoplankton structure in ecologically diverse areas of the sea and the role of marine invasive species in the formation of the community were studied on the meridional and latitudinal trans-Caspian sections in the autumn period of 2008, 2009, and 2012. It was established that the transformation of the phytoplankton community continues in the Caspian Sea, associated with the entry of the Black Sea diatoms Chaetoceros peruvianus, Cerataulina pelagica, and Pseudo-nitzschia seriata into their composition. During the autumn bloom of phytoplankton in November 2008, the number of invasive species reached 1.3-2.3 × 10 cells/L, C. peruvianus and P. seriata to the total weight biomass of the community reached 49-50%. The highest abundance of invasive species was recorded in the shelf areas of the Middle Caspian Sea in its eastern ( C. peruvianus , 2.3 × 10 cells/L), western ( P. seriata , 1.4 × 10 cells/L), and northern ( C. pelagica , 1.3 × 10 cells/L) parts. The north boundary of the distribution of these species in the Caspian Sea was the 5.0 isohaline, which coincided with the highly productive frontal zone (4.0-6.0) of the marginal filter of the Volga River. For the first time, it was shown that the C. peruvianus diatom was a part of the phytoplankton of the upper productive 25-30-meter water layer both in the Middle and in the Southern Caspian during the periods preceding the autumn bloom of phytoplankton (September-October). During that time the most considerable abundance of this species (1.6 × 10cells/L) was recorded in the shallow areas on the Apsheron Sill and the eastern part of the Middle Caspian in the zone of coastal wind upwelling.