In this study we analyzed phytoplankton diversity in 13 environmental samples from Varna Bay (western Black Sea) by using the massively parallel sequencing (MPSS)-based technique as a preliminary study, considering the potential of this technology for future implementation in monitoring programs in the Black Sea. Amplicon sequences of 18S-rRNA gene (V4-5 regions) to study plankton biodiversity were obtained using the Illumina MiSeq 250PE platform. The effective number of sequences deposited in international nucleotide sequence databases of the target region and the amplicon sequence variability are considered as the important factors to influence the taxonomic identification power of the target region. To know the current situation of the taxonomic identification power of the target region, success rates of OTUs and number of MPSSs which were identified as a single species in each supergroup by Blast search were calculated. In Alveolata, Stramenopiles and Opisthokonta, the most dominant supergroups, 22.8, 20.9, 18.6% of the OTUs and 29.0, 50.6, 48.3% of the number of MPSSs were successfully identified as a single species. Surprisingly, success rates of species identification in Archaeplastida, Viridiplantae and Hacrobia showed much higher than those in the dominant supergroups, namely, 55.6, 34.7, 28.9% of the OTUs and 94.5, 46.8, 63.1% of the number of MPSSs, respectively. On the contrary, Amoebozoa, and Excavata data showed lower success rate for species identification than other groups, i.e. 8.3, 11.1 and 5.0, 7.3%, respectively. Therefore, the average success rates of the number of OTUs and the MPSSs were 21.9 and 38.6%, respectively. These data show that >200 eukaryotic species were successfully detected throughout this study, suggesting the effectiveness of the MPSS-based survey for plankton monitoring.