Heat stress is one of the major factors reducing potato yield by limiting the plant photosynthesis activity, production and partitioning of assimilates to the sink. Potato wild relatives (Solanum sect. Petota) are a natural reservoir of valuable traits for abiotic stress resistance. However, it is necessary to assess the response of wild potato genotypes based on physiological features such as gas exchange, chlorophyll index and chlorophyll fluorescence that are promising candidates to improve crop photosynthesis under adverse conditions. Multivariate approaches on two factor experimental design were used to select the best performing genotypes for most important traits influencing the photosynthetic activity under control and heat stress treatments. The most important traits to be focused on are net photosynthetic rates, transpiration rates, and stomatal conductance along with effective photochemical yield of PSII, Coefficient of photochemical yield of PSII, electron transport rate and Fv/Fm ratio which are highly associated with heat stress conditions. Solanum commersonii accessions (BGB003, BGB009) are more likely to be tolerant to heat stress, followed by S. tuberosum 2x (BGB091, BGB093) and S. chacoense (BGB101). The assessment of wild accessions for photosynthetic traits under heat stress is a reliable way to discriminate the most promising sources of abiotic stress resistance even though they have unreliable tuber traits for the breeding of the potato crop.