Qualitative composition and abundance of both ichthyoplankton and small forms of zooplankton were evaluated by field studies in the northern (the Crimea near Sevastopol) and southern (Sinop region and TEEZ) Black Sea during the summers 2000 and 2001. A tendency of increasing the species richness, abundance of fish eggs and larvae as well as zooplankton (which is the food for fish larvae) was observed over a period of Mnemiopsis leidyi and Beroe ovata co-existence. The eggs and larvae of the Mediterranean migrants—bonito and bluefish appeared again in the coastal waters near Sevastopol, which testified to favourable conditions for the spawning and nutrition of these fish species and their larvae. Aborigen copepod Oithona nana was found in the Crimean coastal waters although earlier in the 1990s it had completely vanished. Although rare in the 1990s copepods Centropages ponticus and Paracalanus parvus appeared in inshore waters as well as Pontellids species. Observed increases in species number and abundance of both ichthyoplankton and small zooplankton (≤500 μm), which promoted survival and development of fish larvae, were attributed to reduced predatory impact of Mnemiopsis on prey zooplankton after the arrival of Beroe in the late 1990s. However, the influence of Mnemiopsis continued to be significant during the short period of its peak occurrence in late summer. When this period coincided with the appearance of fish larvae, a negative impact on their survival could be predicted due to a low concentration of food items for larvae feeding.