In this work we isolated a culturable endophytic aerobic heterotrophic bacterial community from the stem and root tissues of elm trees (Ulmus spp.) and analyzed its fluctuations. A total of 724 bacterial isolates were collected at different times (April, June, September and December) from two elm trees, one infected with Elm Yellows phytoplasmas, and one which was healthy-looking. The isolates were grouped into 82 haplotypes, identified by means of amplified ribosomal DNA restriction analysis (ARDRA) using the restriction enzyme AluI, suggesting that the genetic diversity of the bacterial community was very high. The taxonomic position of the isolates belonging to the twelve main haplotypes, representing more than 72% of the total population, was determined by 16S rDNA sequencing. The main genera were Bacillus, Curtobacterium, Pseudomonas, Stenotrophomonas, Sphingomonas, Enterobacter, and Staphylococcus. The fluctuations in the bacterial community, determined by different parameters (seasonal changes, plant organ, presence of phytoplasmas) were studied, revealing that they were influenced both by variations in temperature (warm or cold according to the season) and by the organ examined (roots or stems). The role of the phytopathogenic status in these fluctuations was also discussed.