Impacts of plant genotype on microbial assemblage in the phyllosphere (above-ground parts of plants, which predominantly consists of the set of photosynthetic leaves) of Vitis vinifera cultivars have been studied previously but the impact of grape species (under the grape family Vitaceae) was never investigated. Considering the fact, that the phyllosphere microbiome may have profound effects on host plant health and its performance traits, studying the impact of grape species in microbial taxa structuring in the phyllosphere could be of crucial importance. We performed 16S and ITS profiling (for bacteria and fungi respectively) to access genus level characterization of the microflora present in the leaf phyllosphere of five species within this plant family, sampled in two successive years from the repository situated in the Mediterranean. We also performed α and β-diversity analyses with robust statistical estimates to test the impacts of grape species and growing year, over a two-year period. Our results indicated the presence of complex microbial diversity and assemblages in the phyllosphere with a significant effect of both factors (grape species and growing year), the latter effect is being more pronounced. We also compared separate normalization methods for high-throughput microbiome data-sets followed by differential taxa abundance analyses. The results suggested the predominance of a particular normalization method over others. This also indicated the need for more robust normalization methods to study the differential taxa abundance among groups in microbiome research.