Toxic effects of photochemical smog on ponderosa and Jeffrey pines in the San Bernardino Mountains were discovered in the 1950s. It was revealed that ozone is the main cause of foliar injury manifested as chlorotic mottle and premature needle senescence. Various morphological, physiological and biochemical alterations in the affected plants have been reported over a period of about 40 years of multidisciplinary research. Recently, the focus of research has shifted from studying the effects of ozone to multiple pollutant effects. Recent studies have indicated that the combination of ozone and nitrogen may alter biomass allocation in pines towards that of deciduous trees, accelerate litter accumulation, and increase carbon sequestration rates in heavily polluted forests. Further study of the effects of multiple pollutants, and their long-term consequences on the mixed conifer ecosystem, cannot be adequately done using the original San Bernardino Mountains Air Pollution Gradient network. To correct deficiencies in the design, the new site network is being configured for long-term studies on multiple air pollutant concentrations and deposition, physiological and biochemical changes in trees, growth and composition of over-story species, biogeochemical cycling including carbon cycling and sequestration, water quality, and biodiversity of forest ecosystems. Eleven sites have been re-established. A comparison of 1974 stand composition with data from 2000 stand composition indicate that significant changes in species composition have occurred at some sites with less change at other sites. Moist, high-pollution sites have experienced the greatest amount of forest change, while dryer low-pollution sites have experienced the least amount of stand change. In general, ponderosa pine had the lowest basal area increases and the highest mortality across the San Bernardino Mountains.