The marine dinophyte genus Azadinium is the primary producer of azaspiracids (AZAs) that cause azaspiracid poisoning illness to humans. Until now, more than 60 AZA analogues have been identified, yet the transcriptomic features of this genus are still poorly understood, and the biosynthesis of AZAs remains unknown. Therefore, a whole transcriptome comparative study of two toxic strains of Azadinium poporum, TIO256 (A. poporum ribotype A2 from the Mediterranean Sea) and AZF25 (A. poporum ribotype B from East China sea), and two non-toxic Azadinium species, TIO420 (A. poporum ribotype A2 from Greece) and Azadinium zhuanum (TIO213 from the East China Sea) was performed. The non-toxic Azadinium strains were shown to have larger transcriptomic sizes (TIO420, 109.63Mb; TIO213, 113.85Mb) when compared to the toxic strains (TIO256, 107.54Mb; AZF25, 98.77Mb). The strains possessed G+C contents in the range of 59-61%. Transcriptomic comparative analysis revealed that the unique genes for each strain of AZFC25, TIO256, TIO420, and TIO213 consisted of 41,651 (32.97%), 4,028 (3.29%), 8,639 (6.82%) and 72,762 genes (44.24%), respectively. While 58,444 homologous genes (35.54-47.77%) were commonly shared among all these four strains. A total of 1,556 unique genes were expressed only in the toxic strains, and among them, only 2,878 genes were found in Az. poporum strain but not in A. zhuanum. Functional genes such as ATP binding, DNA binding, and double-stranded DNA binding genes were highly expressed in the toxic strains as compared to the non-toxic strains, suggesting that the toxic Azadinium required higher ATP intercellularly. This study advances our current knowledge of transcriptomic features of the toxic and non-toxic Azadinium which is crucial in clarifying the AZA biosynthesis in Azadinium species.