The course of hypertension remains poorly understood, although impairment of the sympathetic nervous systems is thought to play a role in its aetiology. In this study, RNA-sequencing (RNAseq) was used to identify transcriptomal differences in the sympathetic stellate ganglia between 16-week-old normotensive Wistar rats and spontaneously hypertensive rats (SHR). Sequencing quality was assessed by FastQC and quasi-mapping rate by Salmon. Differential expression results were confirmed by real time reverse transcriptase Quantitative Polymerase Chain Reaction (qRT-PCR). RNAseq analysis was found to be predictive and representative of transcriptomal changes when compared to qRT-PCR by correlation analysis. Whether these changes underpin physiological sympathetic phenotypes associated with hypertension remains to be established, however this dataset identifies lead transcripts as a priori targets for further investigation.