<p>The Metropolitan Area of São Paulo (MASP) in southern Brazil is impacted by high ozone levels posing significant threats to its urban forests and the Atlantic Forest remnants. These green areas, covering 540 km² and constituting 30% of MASP’s territory, necessitate an urgent assessment of air pollution impacts on their flora. Our study investigates the effects of atmospheric pollution on the morphoanatomical and physiological responses of four native tree species (<i>Alchornea sidifolia</i>, <i>Casearia sylvestris</i>, <i>Guarea macrophylla</i>, and <i>Machaerium nyctitans</i>) across two Atlantic Forest remnants in MASP. We examined visual and morphoanatomical changes in leaves, gas exchange, photosynthetic pigments, and plant volatile organic compounds to identify markers for biomonitoring urban environments. Our results reveal that MASP vegetation is adversely affected by tropospheric ozone. Species with porous mesophyll structures, such as <i>M. nyctitans</i> and <i>G. macrophylla</i>, exhibited greater visual and structural damage. In contrast, species with compact mesophyll, such as <i>A. sidifolia</i> and <i>C. sylvestris</i>, demonstrated higher tolerance. This suggests that anatomical architecture critically influences species’ responses to atmospheric pollutants, such as tropospheric ozone. Additionally, we propose that ozone influx occurs through both stomatal pathways and as a result of direct and indirect injuries to the plant tissues. Additionally, our study identifies non-visual markers, including anatomical and physiological parameters and plant volatile organic compounds (e.g., presence of salicylates), as effective tools for monitoring plant species in urban environments. These insights highlight key anatomical and metabolic markers that help distinguish ozone-tolerant species from sensitive species, providing valuable information for monitoring air pollution in urban forests.</p>