The cDNA of okra (flowers and fruits) were sequenced based on Illumina Hiseq 2500 and were analyzed by using the bioinformatics methods subsequently, such as sequencing assess and gene function annotation. The result of research shows that: (1) 7.12 Gb and 8.14 Gb Clean Data were obtained respectively from the flowers and fruits and the base ratios with quality values higher than 30 in reads (Q30) were more than 91.0% from both. (2) Compared the transcriptome of the flowers and fruits, 1 131 differentially expressed genes (DEGs) were found, including 319 upregulated genes and 1 017 downregulated genes. (3) Annotation analysis indicated that 1 131 genes were annotated. With GO function annotation classification, 455 functional annotations of these DEGs were divided into 41 function categories, in which many function categories were mainly involved, such as metabolic process, catalytic activity, singleorganism process, cellular process. Through KOG analysis, there were 472 functional annotations of DEGs, involving 23 functional classifications. KEGG analysis showed that 372 DEGs were annotated to 80 metabolic pathways, and obtained 10 key DEGs, F3H, F3′5′H, DFR, ANR, ANS, GT, LAR. F3H and DFR showed upregulated effect in okra flowers; F3′5′H, ANR and LAR showed downregulated effect in okra fruits; ANS and GT showed up/downregulated effects in flowers and fruits. (4) The relative expression levels of 7 DEGS wasin line with that of the transcriptional group by qRTPCR. (5) Through the flavonoid metabolic pathway, the research showed that anthocyanin were catalyzed by F3H, DFR, ANS(c83240), GT (c82265/c82004) from NAR in okra flowers; The formation of DHM was initiated by F3′5′H, then produced flavonols by FLS; Partly NAR was catalyzed by F3H and DFR to dephinidin, then ultimately went into anthocyanins and proanthocyanidins synthesis pathways. This study enriched transcriptome information of okra and provided reference for the purification and functional utilization of flavonoids in okra.