Persimmon fruit accumulates a quantity of proanthocyanidins (PAs) into "tannin cells" during development. In order to isolate genes involved in PA accumulation, suppression subtractive hybridization (SSH) libraries were constructed from astringent and non-astringent fruit as tester and driver populations for reciprocal SSH procedures. Three populations; (i) the fruit of F1 individuals derived from the cross between Chinese and Japanese PCNA, (ii) BC1 individuals derived from the cross between F 1 (Japanese PCNA × astringent cultivar) and Japanese PCNA, and (iii) astringency-removed fruit on the tree by ethanol treatment and untreated astringent fruit, were used for the SSH analysis. We identified several cDNA fragments which have similarity to flavonoid biosynthetic genes, such as PAL CHS, DFR and ANR. Additionally, we isolated gene fragments including F3GalTase, DHQ/SDH, SCPL, 1-CysPer and GST, which have not been identified for their role in PA biosynthesis. RNA gel blot analysis revealed that these genes were coincidentally expressed with PA accumulation during fruit development both in astringent and PCNA types. These genes, identified as being differentially expressed in astringent fruit by SSH, may help further study on the molecular mechanism of PA biosynthesis and its accumulation in tannin cells.