Food security is a major concern of the 21st century, given climate change and population growth. In addition, high salt concentrations in soils affect ~20% of irrigated land and cause a substantial reduction in crop yield. Cultivating salt-tolerant crops could enable the use of salt-affected agricultural land, reduce the use of fresh water and alleviate yield losses. Innovative methods need to be developed to study traditional and novel traits that contribute to salinity tolerance and accurately quantify them. These studies would eventually serve for developing new salt tolerant crops, adapted to the harsh arid and semi-arid climate conditions. A study of 200 accessions of the wild tomatoes (Solanum pimpinellifolium) was conducted in field conditions with phenotyping using an unmanned aerial vehicle (UAV)-mounted hyperspectral camera. Six genotypes with different levels of salt tolerance were sampled for leaf pigment analyses, revealing a clear pattern for the high salt tolerant accession M007, where pigment content in the salt-treated plants significantly increased compared to their control counterparts only in harvesting campaigns 3 and 6, each performed two days after the first and second salt stress application events. Moreover, the light harvesting capacity was found to be better maintained under salt stress in the medium (M255) and highly salt tolerant (M007 and M061) accessions. Pigment quantitation data will contribute towards the groundtruthing of hyperspectral imaging for the development of remote sensing-based predictive pigment mapping methods. This work establishes a reliable quantification protocol for correlating pigment content with vegetation indices. Hence, pigment content captured by imaging techniques and validated using biochemical analysis would serve in developing a high-throughput method for pigment quantitation in the field using UAV-based hyperspectral imaging. This would serve as a tool for measuring pigment content in large number of genotypes in the field which would eventually lead to new salt-tolerant genes.