Roots of eggplant (Solanum melongena L.) cv. Pingtong Long Eggplant (EG117) were subjected to ten flooding treatments. Messenger RNAs from plants subjected to flooding periods for 0.25 to 1 and 3 to 12 h as well as unflooded plants (control) were used as the tester and driver samples, respectively. Following suppression subtractive hybridization, polymerase chain reaction (PCR) products were ligated into a cloned vector for Escherichia coli-competent cell transformation, followed by nested PCR screening of positive cDNA inserts. PCR products of these unique clones were digested with Sau3AI to identify any differentially displayed banding patterns. Recombinant cDNA clones were then picked for plasmid extraction and then sequenced. Using BLAST and Gene Ontology database searches, 25 of these unigenes were found to be involved in metabolism, regulation, stress, and development categories, whereas nine novel genes with unknown functions that may have potential roles in flooding stress in eggplant were also identified. Five differentially expressed gene transcripts with known functions were randomly selected for real-time reverse-transcription quantitative PCR to investigate plants subjected to flooding stress from 0 to 72 h. All genes were upregulated in flood treatments (15 min to 72 h) when compared to the control. These findings indicated that flood-induced genes were closely related to various metabolic pathways and involved in genetic regulation of flood stress response.