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<i>Stevia rebaudiana</i> (Bertoni) is a highly valuable crop for the steviol glycoside content in its leaves, which are no-calorie sweeteners hundreds of times more potent than sucrose. The presence of health-promoting phenolic compounds, particularly flavonoids, in the leaf of <i>S. rebaudiana</i> adds further nutritional value to this crop. Although all these secondary metabolites are highly desirable in <i>S. rebaudiana</i> leaves, the genes regulating the biosynthesis of phenolic compounds and the shared gene network between the regulation of biosynthesis of steviol glycosides and phenolic compounds still need to be investigated in this species. To identify putative candidate genes involved in the synergistic regulation of steviol glycosides and phenolic compounds, four genotypes with different contents of these compounds were selected for a pairwise comparison RNA-seq analysis, yielding 1136 differentially expressed genes. Genes that highly correlate with both steviol glycosides and phenolic compound accumulation in the four genotypes of <i>S. rebaudiana</i> were identified using the weighted gene co-expression network analysis. The presence of UDP-glycosyltransferases <i>76G1</i>, <i>76H1</i>, <i>85C1</i>, and <i>91A1</i>, and several genes associated with the phenylpropanoid pathway, including <i>peroxidase</i>, <i>caffeoyl-CoA O-methyltransferase</i>, and <i>malonyl-coenzyme A:anthocyanin 3-O-glucoside-6″-O-malonyltransferase</i>, along with 21 transcription factors like <i>SCL3</i>, <i>WRK11</i>, and <i>MYB111</i>, implied an extensive and synergistic regulatory network involved in enhancing the production of such compounds in <i>S. rebaudiana</i> leaves. In conclusion, this work identified a variety of putative candidate genes involved in the biosynthesis and regulation of particular steviol glycosides and phenolic compounds that will be useful in gene editing strategies for increasing and steering the production of such compounds in <i>S. rebaudiana</i> as well as in other species.