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A cDNA library was constructed from satsuma mandarin (Citrus unshiu Marc.) fruit tissues during the rapid cell enlargement phase. A total of 950 individual cDNA clones was partially sequenced and compared with GenBank databases for characterizing the gene repertoire expressed during this developmental phase. Among these, 426 cDNA clones (44.8%) showed sequence identity with previously characterized genes with optimized (OPT) scores of ≥200, while 524 clones (55.2%) resulted in low OPT scores (<200) and did not show any significant sequence identity with previously published genes. Based on nucleotide sequence, most clones with OPT scores of ≥200 were assumed to be transcription-, translation-, cell-wall-metabolism-, and stress-response-related genes. Other clones showed homology with published sequences related to housekeeping and stress-response-related genes, including metallothionein-like proteins, late-embryogenesis-abundant (LEA) proteins, and heat-shock proteins. These results suggested that Citrus fruit during rapid cell enlargement were metabolically active and expanding in response to biotic and abiotic stress. For clones with low nucleotide sequence homology, the recurrence was evaluated by aligning nucleotide sequences of each clone and generating contig maps. Expressed sequence tags (ESTs) of 162 clones with OPT scores <200 have not been reported for any other organism. Collectively, randomly sequenced cDNA clones described in this study provided information on types of genes expressed during the rapid cell enlargement phase in Citrus fruit. These genes should be used as candidates for Citrus genome mapping projects.