The molecular basis for the adaptation of fruit tissues to low oxygen treatments remains largely unknown. RT-PCR differential display (DD) was employed to isolate anoxic and/or hypoxic genes whose expression responded to short, low-oxygen regimes. This approach led to the isolation, cloning, successful sequencing, and bioinformatic analysis of 98 transcripts from Citrus flavedo tissues that were differentially expressed in DD gels in response to 0, 0.5, 3, and 21% O₂ for 24 h. RNA blot analysis of 25 DD clones revealed that 11 genes were induced under hypoxia and/or anoxia, 11 exhibited constitutive expression and three transcripts were suppressed by low oxygen levels. Almost half of the DD cDNAs were either of unknown function or shared no apparent homology to any expressed sequences in the GenBank/EMBL databases. Six DD genes were similar to molecules of the following functions: C-compound and carbohydrate utilization, plant development, amino acid metabolism, and biosynthesis of brasinosteroids. Time-course and stress-related experiments of low O₂-regulated genes indicated that these genes responded differently in terms of their earliness, band intensity, and their specificity to stresses, showing that some of them can be termed hypoxia- or anoxia-induced genes.