Heavy metals are one of the most important environmental pollutants in all over the world. Heavy metals not only are seen in the soil and water but also can be found in the air. In recent years, the concentration of these metals has been increased in the atmosphere of many cities due to human activities. Examining the qualitative and quantitative changes of the endophyte microorganisms is one of the best markers to investigate the long-term impacts of these pollutants. This research was conducted in order to identify the effect of cadmium, lead and mercury on the population of the endophyte bacteria inside the elm trees in Tabriz. The plant samples including leaf and stem were collected during two years (2015-2016) in two different regions of the city randomly and their endophyte bacteria were isolated. One of the selected sampling site was the central region of the city with the highest pollution and the other one was marginal with less pollution in Tabriz. The experiments showed that there was a significant difference between the bacterial micro flora in these two regions. While, in the elm trees of the marginal region with less pollution the dominated bacteria were Gram negative bacteria, mostly from Pseudomonas genus, though in the polluted area, Gram positive bacteria, particularly Actinomyces and Bacillus were dominated.