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Cassava plants’ response to waterlogging must be monitored in an accurate and timely manner to mitigate the adverse effects of waterlogging stress. Under waterlogging conditions, root hypoxia reduces water uptake and stomatal closure limits transpiration, which often results in increased leaf temperature due to reduced evaporative cooling. However, how this relationship changes in cassava leaves under waterlogged conditions remains poorly known. This study hypothesized that a cooler canopy is more critical for better performance under waterlogging stress in various cassava genotypes. Two cassava cultivars were subjected to twelve days of waterlogging. The experiment was laid out in a completely randomized design with three replications. Results revealed a significant decrease in photosynthetic rate, stomatal conductance, and transpiration, and an increase in leaf temperature and ΔT, reflecting impaired stomatal regulation and reduced evaporative cooling. Strong negative correlations between ΔT and photosynthetic parameters were observed presenting ΔT as a reliable, nondestructive indicator of cassava’s physiological responses under hypoxic conditions. Findings indicate that maintaining cooler canopies may contribute to enhanced tolerance and survival under waterlogging. ΔT can be used as a practical screening tool for identifying and selecting waterlogging-tolerant cassava genotypes. However, further studies involving contrasting cultivars and additional parameters such as leaf relative water content, free water content, and leaf anatomy are recommended to validate and strengthen reported findings.