Stone fruit trees are economically important crops in Italy, particularly in the southern regions. Different diseases can affect these trees, and bacterial diseases cause significant economic losses, reducing yield and rendering fruits unmarketable. This study aimed to assess the bacterial diversity in different aerial organs of almond, cherry, and peach trees in orchards located in four different areas of Bari Province (Apulia, Italy). Samples were collected at the end of March and May and 193 isolates were obtained. Based on the morpho-taxonomic characteristics, isolates were grouped in 14 different morphotypes. Considering the occurrence of all morphotypes for each sampling time, according to the multivariate analysis, significant differences (p>0.05) were observed among morphotypes, plant orchards, and locations. Based on biochemical characterization (KOH, fluorescence, LOPAT and Urease tests) performed on 52 isolates representative of the 14 morphotypes, 16 biochemical profiles, generally corresponding to nonpathogenic bacteria, were identified. Additionally, one representative isolate for each morphotype was characterized by molecular analysis of the 16S rDNA partial sequence, and only for the morphotypes M2 and M9, two isolates each were used. Pseudomonas was the most represented genus (six morphotypes), followed by Curtobacterium, Sphingomonas, Rhodutorula (two morphotypes), and Pantoea and Hannaella (one morphotype). In conclusion, the data presented here provide an important new overview of the bacteriome present on the aerial organs of important stone fruit species in the province of Bari, also considering the ongoing climatic change. In addition, the isolated bacteria can represent a source of beneficials in an ecosystem service well adapted to the species and climate change.