The effects of ozone on ozone-sensitive (NC-S) and ozone-resistant (NC-R) clones of Trifolium repens L. cv. Regal are compared at ultrastructural level by Transmission Electron Microscopy (TEM). Each clone were exposed to ambient ozone levels in the Botanical Garden of Rome, Italy, according to the ICP Vegetation Experimental Protocol (2005). TEM analyses showed that ultrastructural injuries appeared to be widespread in NC-S leaves. On the contrary, the NC-R clones showed much less damage: the chloroplast maintained an almost intact organisation of thylakoids, but the chloroplast side facing the apoplastic space appeared with no thylakoids. Interestingly, Hsp70 levels, an important stress marker, were only slightly increased in the ozone-sensitive clone with respect to the ozone-resistant clone; in contrast, a strong decrease (−60%) in phosphoenolpyruvate carboxylase (PEPCase) protein levels was measured in the NC-R clone. These data are discussed in the frame of the proposed ozone toxicity mechanism.