Soil and water salinization has global impact on the sustainability of agricultural production, affecting the health and condition of staple crops and reducing potential yields. Identifying or developing salt-tolerant varieties of commercial crops is a potential pathway to enhance food and water security and deliver on the global demand for an increase in food supplies. Our study focuses on a phenotyping experiment that was designed to establish the influence of salinity stress on a diversity panel of the wild tomato species, Solanum pimpinellifolium . Here, we explore how unoccupied aerial vehicles (UAVs) equipped with both an optical and thermal infrared camera can be used to map and monitor plant temperature (T p ) changes in response to applied salinity stress. An object-based image analysis approach was developed to delineate individual tomato plants, while a green-red vegetation index derived from calibrated red, green, and blue (RGB) optical data allowed the discrimination of vegetation from the soil background. T p was retrieved simultaneously from the co-mounted thermal camera, with T p deviation from the ambient temperature and its change across time used as a potential indication of stress. Results showed that T p differences between salt-treated and control plants were detectable across the five separate UAV campaigns undertaken during the field experiment. Using a simple statistical approach, we show that crop water stress index values greater than 0.36 indicated conditions of plant stress. The optimum period to collect UAV-based T p for identifying plant stress was found between fruit formation and ripening. Preliminary results also indicate that UAV-based T p may be used to detect plant stress before it is visually apparent, although further research with more frequent image collections and field observations is required. Our findings provide a tool to accelerate field phenotyping to identify salt-resistant germplasm and may allow farmers to alleviate yield losses through early detection of plant stress via management interventions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Stutsel, Johansen, Malbéteau and McCabe.)