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This dissertation was written as part of the MSc in Bioeconomy: Biotechnology and Law at the International Hellenic University. The aim of this study was to identify the bacterial assemblages, the diversity and the relative abundance and dominance of the taxonomic groups found in the phyllosphere and rhizosphere of Solanum lycopersicum plants in two fields. This cultivar was grown in arid volcanic soil of Santorini island of the Mediterranean basin which is characterized by its unique properties. The study was approached with the use of 16S rRNA gene high-throughput amplicon sequencing and a downstream pipeline of bioinformatic analysis. The results showed overall, high bacterial richness with Proteobacteria and Actinobacteria displaying dominance in terms of the number of OTUs. Furthermore, Proteobacteria, Actinobacteria and Cyanobacteria display higher relative abundance in both the plant compartments. Vlichadas’ phyllospheric communities generally differed in composition while also displayed the lowest number of OTUs in the dataset. In conclusion, the bacterial assemblages of both sampling sites consisted of common generalist taxa which had a key role in the survivability of the plants, along with the abundant specialist taxa which were driven by the environmental pressure, while composition was overall similar, the abundance of species differed between samples.