Expressed sequence tag(EST) analysis of the pulp of the red-fleshed mutant ’Cara Cara’ navel orange provided a starting point for gene discovery and transcriptome survey during citrus fruit maturation.Interpretation of the EST datasets revealed that the mutant pulp transcriptome held a high section of stress responses related genes,such as the type Ⅲ metallothionein-like gene(6.0%),heat shock protein(2.8%),Cu/Zn superoxide dismutase(0.8%),late embryogenesis abundant protein 5(0.8%),etc.133 transcripts were detected to be differentially expressed between the red mutant and its orange-color wild genotype ’Washington’ via digital expression analysis.Among them,genes involved in metabolism,defense/stress and signal transduction were statistical overrepresented.Fifteen transcription factors,composed of NAM,ATAF,and CUC transcription factor(NAC);myeloblastosis(MYB);myelocytomatosis(MYC);basic helix-loop-helix(bHLH);basic leucine zipper(bZIP) domain members,were also included.The data reflected the distinct expression profile and the unique regulatory module associated with these two genotypes.Eight differently expressed genes analyzed in digital were validated by quantitative realtime polymerase chain reaction.For structural polymorphism,both simple sequence repeats and single nucleotide polymorphisms(SNP) loci were surveyed;dinucleotide presentation revealed a bias toward AG/GA/TC/CT repeats(52.5%),against GC/CG repeats(0%).SNPs analysis found that transitions(73%) outnumbered transversions(27%).Seventeen potential cultivar-specific and 387 heterozygous SNP loci were detected from ’Cara Cara’ and ’Washington’ EST pool. Expressed sequence tag (EST) analysis of the pulp of the red-fleshed mutant ’Cara Cara’ navel orange provided a starting point for gene discovery and transcriptome survey during citrus fruit maturation. Inprepretation of the EST datasets revealed that the mutant pulp transcriptome held a high section of stress responses related genes such as the type III metallothionein-like gene (6.0%), heat shock protein (2.8%), Cu / Zn superoxide dismutase etc.133 transcripts were detected to be differentially expressed between the red mutant and its orange-color wild genotype ’Washington’ via digital expression analysis. Among them, genes involved in metabolism, defense / stress and signal transduction were statistically overrepresented .Fifteen transcription factors , composed of NAM, ATAF, and CUC transcription factor (NAC); myeloblastosis (MYB); myelocytomatosis (MYC); basic helix-loop-helix (bHLH); basic leucine zipper refle cted the distinct expression profile and the unique regulatory module associated with these two genotypes. Etioned differently expressed genes analyzed in digital were validated by quantitative realtime polymerase chain reaction. For structural polymorphism, both simple sequence repeats and single nucleotide polymorphisms (SNPs) loci were surveyed ; dinucleotide presentation revealed a bias toward AG / GA / TC / CT repeats (52.5%), against GC / CG repeats (0%). SNPs analysis found that transitions (73%) outnumbered transversions specific and 387 heterozygous SNP loci were detected from ’Cara Cara’ and ’Washington’ EST pool.