Chlorophyll and anthocyanin contents provide a valuable indicator of the status of a plant‘s physiology, but to be more widely utilized it needs to be assessed easily and non-destructively. This is particularly evident in terms of assessing and exploiting germplasm for plant-breeding programs. We report, for the first time, experiments with Fragaria chiloensis (L.) Duch. and the estimation of the effects of response to salinity stress (0, 30, and 60 mmol NaCl/L) in terms of these pigments content and gas exchange. It is shown that both pigments (which interestingly, themselves show a high correlation) give a good indication of stress response. Both pigments can be accurately predicted using spectral reflectance indices (SRI); however, the accuracy of the predictions was slightly improved using multilinear regression analysis models and genetic algorithm analysis. Specifically for chlorophyll content, unlike other species, the use of published SRI gave better indications of stress response than Normalized Difference Vegetation Index. The effect of salt on gas exchange is only evident at the highest concentration and some SRI gave better prediction performance than the known Photochemical Reflectance Index. This information will therefore be useful for identifying tolerant genotypes to salt stress for incorporation in breeding programs.