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In order to identify volatile oil synthesis related genes in Illicium verum, transcriptome sequencing and assembly annotation were carried out on the leaves of the superior clone Guijiao 69 and common variety Zhen 01, two varieties with significant difference in volatile oil content. Then GO and KEGG pathways analyses of differentially expressed genes (DEGs) were performed. The results were as follows: (1) A total of 84 182 Unigenes were obtained after transcripts assembly, and 59 161 Unigenes were annotated in NR, NT, Swissprot, KEGG, KOG, GO, and Pfam databases. A total of 30 572 DEGs were obtained after filtering the low abundance genes, and 15 025 up-regulated and 15 547 down-regulated genes were identified in Guijiao 69 compared to the common variety Zhen 01. (2) GO classification results showed that 20 287 DEGs were annotated. In addition, 21 600 DEGs were involved in 133 KEGG pathways. Among them, genes encoding the key enzymes related to volatile oil synthesis such as linalool synthase, myrcene synthase, geranyl geranyl pyrophosphate synthase, cinnamoyl CoA reductase, caffeic acid 3-O-methyltransferase and cinnamyl alcohol dehydrogenase were differentially expressed and enriched in monoterpene biosynthesis pathway, terpene skeleton biosynthesis pathway and phenylpropanoid biosynthesis pathway. (3) Transcription factor analysis showed that the DEGs were distributed in 31 transcription factor families, of which MYB family had the most Unigenes. In this study, transcriptome sequencing was performed to analyze the DEGs superior clones and common varieties of I. verum as well as their related functions and pathways. The candidate genes obtained provide the references for further exploring the synthesis mechanism of characteristic components of volatile oil and molecular breeding of I. verum.