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The monitoring studies carried out in the southern Romanian Carpathians (Retezat and Bucegi - Piatra Craiului Mts) provide a scientific support for long term ecosystem research (LTER). Their general objective is to characterize the air pollution and its potential effects upon forest ecosystems’ status and biodiversity in close connection with climatic changes. Two monitoring networks were placed in selected forest ecosystems for each LTER site (11 plots in Retezat and 22 plots in Bucegi - Piatra Craiului, respectively). Both in Retezat and Bucegi - Piatra Craiului Mts, the distribution of mean ozone (O3) concentrations are significantly correlated with altitude. The location (plot) has a significant influence on ozone concentration and in some cases the exposure period along the growing season has an influence. Ambient ozone (O3) and ammonia (NH3) concentrations were below toxicity levels for forest trees, their health status (crown condition) and volume growth being insignificantly affected. More than 45% of the rain events were acidic with pH≤5.5, thus contributing to an increased N deposition on forest stands. In Retezat Mts crown condition was relatively better than in Bucegi - Piatra Craiului Mts. As a consequence, in 2009 European beech (Fagus sylvatica) was the least affected species, with a percentage of damaged trees (crown defoliation higher than 25%) between 8.0% (Retezat) and 9.8% (Bucegi - Piatra Craiului), followed by Norway spruce (Picea abies) with 12.9% (Retezat) and 27.7% (Bucegi - Piatra Craiului). The most affected species was Silver fir (Abies alba) with 31.6% of damaged trees (Bucegi-Piatra Craiului). In the last period, both European beech and conifers (Norway spruce and Silver fir) with high defoliation (damaged trees) had lower annual relative increment than trees with low defoliation (healthy trees). A definite trend regarding rapid environmental modifications is not evident and no significant reduction of biodiversity occurred. In addition, all the vegetation biodiversity components of the forest ecosystems are specific to the stand type’s structures and local climate conditions, and no quantifiable consequences of specific air pollutants on ecosystems’ diversity occurred.