Abstract: Genetic variabilities of the low-acid mutants and late-mature mutant of the Fengjie navel orange were examined by AFLP technology .By using 64 pairs of selective primers ,5336 bands ,among them , 7 specific bands in low-acid mutant ,2 specific bands in late-mature mutant were detected. The sequencing of these specific bands and their Blastp analysis showed :the trait of low acid in fruit in the low-acid mutant of Fengjie navel orange could result from the deficiency or mutation of the gene encoding Na+/H+ antiporter-like protein, while the deficiency or mutation of the genes encoding the flower development protein cycloidea (cyc3) and cytoplasmic aconitate hydratase could be responsible for the late mature of late-mature mutant .