To insert maize crop in the lowlands, the National Maize and Sorghum Research Center has developed, through the recurrent phenotypical selection, a maize variety called Saracura-BRS-4154, which has the capability to survive in periods of flooding. This study was carried out with the purpose of characterizing young plants of successive selection cycles of the variety ‘Saracura’, under flooding, concerning the morpho-physiology. The assay was carried out in greenhouse by sowing 10 alternate selection cycles and a BR 107 variety known for its susceptibility to flooding. It was found that the last selection cycles resulted in a greater development of thin roots, greater volume and root length. The selection cycles decreased the exodermis and increased aerenchyma formation in the roots over time. There was also leaf plasticity throughout the cycles, and it was noted an increase in the gas exchange parameters and also in the stomata number and size. Our results showed that there was a genetic gain in the morpho-physiological changes related to flooding throughout the selection cycles of ‘Saracura’ maize young plants.