Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharma-ceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of as-sembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated trans-criptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled trans-criptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive trans-cripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. har-mala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto En-cyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their po-tential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.