Nonnative Phragmites australis (common reed) is widely distributed across North America and insufficient knowledge of P. australis has impeded the efficiency of management. To aid in Phragmites management and future studies, we used RNA-seq data from multiple types of plant tissue to construct forty-nine P. australis transcriptomes via different assembly tools and multiple parameter settings, resulting in seven assembled transcriptomes for further comprehensive assessments. The optimal transcriptome ("cd-hit") was selected for functional annotation and downstream analyses. This data release contains the seven assembled transcriptomes, and data derived from the optimal transcriptome (functional annotations, tissue-specific expression patterns, putative transcription factors, and simple sequence repeats markers).