Two transcriptome assembly strategies (mapping-first and de novo assembly-first) were used in this study to evaluate the applicability on transcriptome study for common carp varieties, using Oujiang color common carp as studied species. Regarding the transcriptome assembly and annotation, our study showed the average length of assembled transcripts using mapping-first strategy (Cufflinks software) was 1 545 bp, the number of annotated transcripts was 77 601. The average length of transcript assembled using de novo assembly-first strategy (Trinity software) was 979 bp, the number of annotated transcripts was 69 406. Considering the gene structure and alternative splicing prediction, our results presented three and four alternative splicing transcripts for every gene for Cufflinks and Trinity assembly, respectively (P<0.001). Meanwhile, the gene structure prediction was more accurate in Cufflinks assembly than Trinity assembly. Our results indicated the longer transcripts, the more annotated transcripts, and transcripts with more accurate gene structure were identified in the transcriptome assembled using mapping-first strategy (Cufflinks software), which is more suitable for the following gene expression analysis. On the contrary, the transcriptome assembled using de novo assembly-first strategy (Trinity software) provided more accurate specific gene sequences, which is vital for evolutionary studies of Oujiang color common carp. Our study demonstrated that both assembly strategies were essential for the Oujiang color common carp transcriptome, and provided guidance for the choice of transcriptome assembly strategies on other varieties of common carp.