Okra (Abelmoschus esculentus) is a heat tolerant vegetable crop with high economic and nutritional importance in parts of Asia, Africa, and America. The okra biodiversity held in gene bank collections could be mined for traits for breeding more stress tolerant and nutritional cultivars. An okra core collection of 166 accessions comprising A. esculentus, A. moschatus, A. caillei, and A. manihot has been assembled from the World Vegetable Center germplasm collection (840 accessions) based on diversity analysis with 20 microsatellite markers. A selection of A. esculentus accessions of the core collection (75 accessions) and 20 breeder-selected genotypes have been screened for variation of their response to flooding stress under field conditions using a high throughput phenotyping system. Growth increment per day and changes of physiological indices were measured before, during, and after application of 9 days of flooding stress. Several accessions showed only a small reduction in daily growth increment during flooding. Across the germplasm panel, maintained growth was correlated with maintained normalized differential vegetation index and was negatively correlated with plant senescence index. Accessions with maintained growth and health under flooding were selected for future further analysis and use in breeding.