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Carotenoids play two important roles in a photosynthesis such as light-harvesting and photoprotection. Two excited electronic states, optically bright 1Bu+ and dark 2Ag-, respectively, are crucial for these processes. While these states have very different electronic structure, they both have to be described at similar level of accuracy to effectively model an energy transfer in photosynthesis. We have recently shown that a novel multi-reference perturbation theory MR-DSRGPT2 combines moderate computational complexity and accuracy for description of low-lying excited states of polyenes. In this work we expanded a range of model objects to natural polyenes proving that MR-DSRGPT2 can be used as an effective tool for modeling of their excited states. Vertical and adiabatic excitation energies were calculated for the 1Bu+ and dark 2Ag- electronic states for six natural polyenes, three open-chain (neurosporene, spheroidene, and lycopen) and three closed-chain (lutein, violaxanthin, and zeaxanthin). Nuclear geometries for the ground and 1Bu+ states were optimized by means of (TD)DTF. We proposed spin-flip DFT for optimization the 2Ag- state instead of DMRGSCF used earlier, since spin-flip DFT successfully accounts for multiconfigurational nature of the 2Ag- state. State-averaged DMRSCF in an active space of the entire π-system followed by MR-DSRGPT2 correction was used to calculate electronic states energies for respective nuclear geometries. The proposed approach allowed to conserve comparable accuracy with previous results for polyenes but with lesser computational complexity allowing to treat natural carotenoids.