Maize (Zea mays L.) is an economically valuable crop grown widely across the world. It is very sensitive to soil flooding and submergence/waterlogging which leads to yield loss and can result in death of the plant. Variation in precipitation patterns and increased flooding due to climate change may result in lower overall maize productivity in afflicted areas. Since maize is one of the world’s most planted crops and a staple for millions, it is very important to develop improved varieties of maize to cope with the increasing stress. Maize is an ancient allopolyploid and shares this event with other members of the genus Zea and the genus Tripsacum. Recently, Vossia cuspidata (Roxb.) Griff. (hippo grass) was suggested as a putative, extant relative of one of Zea/Tripsacum’s diploid progenitors. The parental relative Vossia cuspidata and close relatives Zea nicaraguensis H.H.Itis and B.F. Benz and Tripsacum dactyloides L. show increased tolerance to submergence/waterlogging stress compared to cultivated maize, which are all likely independently evolved traits. Several flood tolerant quantitative trait loci have been identified in maize inbred lines suggesting maize may have the capacity for flooding-tolerance. The study aims to examine the evolution of flooding tolerance in maize using extant parental and wild relatives. To do this, we designed a greenhouse experiment using one flooding-sensitive maize inbred line and three flooding-tolerant wild relatives. The studied species were subjected to three different flooding treatments and a total of 72 root and leaf tissue samples were collected for RNA extraction, transcriptome library preparation, and sequencing. We have used the sequencing data to investigate whether gene expression and recruited molecular pathways differ in maize compared to wild relatives in response to flooding, specifically focusing on how paralog retention and usage differs between species of varying responses. We also conducted phylogenetic analysis of the differentially expressed genes to answer how the flooding response traits evolved in maize. Initial results suggest that these species have very different responses to prolonged flooding, with the aquatic Vossia having the most distinction. The identification of flooding tolerance genes will potentially help to develop flooding-tolerant cultivars, while the comparison of a crop to wild relatives demonstrates the need for crop scientists to look to nature for solutions to agricultural problems.