Arabidopsis arenosa is closely related to Arabidopsis halleri, which is a model plant species used to study the adaptation to environments highly contaminated with trace metal elements (TME). Tolerance to Cd and Zn has only been largely studied in A. halleri , while in A. arenosa is neglected. In this study, we compared the impact of high Cd or Zn doses on the photosynthetic apparatus of two A. arenosa and A. halleri ecotypes growing on the same contaminated site in southern Poland. Plants were grown in hydroponic culture during six weeks, and then treated with 1.0 mM Cd or 5.0 mM Zn for 5 days. Chlorophyll a fast fluorescence transients and pigment content were measured after 0, 24, 48, 84 and 120 h of treatment. In both species, exposure to TME excess caused a decrease in chlorophyll and an increase in anthocyanin contents in leaves compared with control conditions. The maximum quantum efficiency of the PSII (φP0) was significantly lower after 84 h Cd treatment in A. halleri and after 120 h in A. arenosa. Zn treatment significantly lowered φP0 in A. halleri after 120 h, while it had no impact in A. arenosa. After 5 d Cd treatment, the energy absorbance, electron transport flux and the percentage of active reaction centres decreased more in A. arenosa than in A. halleri. However, the electron transport flux was less affected in than in the second species. Zn treatment had comparatively less toxic effect than Cd excess on A. halleri and it caused only a decrease in the electron transport flux. On the other hand, A. arenosa plants treated with Zn excess reacted as strongly as with Cd and all energy fluxes significantly decreased. The two species showed contrasting behaviour in TME accumulation. A. arenosa accumulated almost three times more Cd in shoots than A. halleri. On the opposite, three-fold higher Zn concentration was measured in A. halleri leaves compared to A. arenosa. Our results supported hyper-tolerance of both species to high Cd or Zn doses. However, the photosynthetic apparatus of two metallicolous tested ecotypes responded differently to the TME treatments. Our research can improve knowledge on TME tolerance and accumulation in plants, and this may help improving biofortification and phytoremediation strategies.