Flooding is an abiotic environmental stress. Flooding stress resulted in the changes of aerobic to anaerobic conditions. Adaptation of plants to flooding stress can be seen on the changes of the anatomy, morphology, and metabolic mechanisms. This study aimed to observe changes in the anatomy of the root conjunction with some agronomic under flooding in four maize cultivars. The research was arranged in Factorial Randomized Complete Block with three replications. The maize cultivars, namely Gumarang, Bima5, Bisi 2, and Bisma were flooded respectively and a control is not stagnant. The 21-day plants were inundated at a high level of 5 cm from surface for 10 days. Cultivars showed tolerant response to flooding stress. Flooding stress increased the percentage of cavity aerenchyma on all cultivars. Flooding affected the growth and the development of agronomic characters of maize crops. Plant height, stem diameter, and number of leaves decreased at all maize cultivars. Keywords: root, anatomy, agronomy, flooding, maize