Glehnia littoralisis an important medicinal halophyte—the dried root of which is used as Chinese herbal medicine. However, the use, selection and stability of reference genes are rarely verified in studies ofG. littoralis, which hampers investigation of its salt tolerance and metabolism. In this study, we selected 13 candidate reference genes from the transcriptome data ofG. littoralis—serine/threonine-protein phosphatase PP2A (PP2A), polyubiquitin 10 (UBQ10), actin (ACT), elongation factor 1-α (EF1-α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), α-tubulin (α-TUB), β-tubulin (β-TUB), polypyrimidine tract-binding protein 1 (PTBP1), expressed protein 1 (EXP1), expressed protein 2 (EXP2), TIP41-like (TIP41), SAND family (SAND), and cyclophilin 2 (CYP2), and used qRT-PCR to analyse their expression levels in roots ofG. littoralistreated with NaCl, polyethylene glycol (PEG), abscisic acid (ABA), and methyl jasmonate (MeJA), as well as in various organs ofG. littoralis. The ΔCt, geNorm, NormFinder, and BestKeeper algorithms were used to assess the expression stability of the candidate reference genes and the results were then used to generate a comprehensive rank list with the RankAggreg R package. The most stable reference genes for normalisation wereEXP1andPP2Ain response to NaCl,EXP2andPP2Ain response to ABA,CYP2andα-TUBin response to MeJA, andACTandEXP1in the PEG and the organ subsets.GAPDH,β-TUB, andUBQ10exhibited low stability and so were unsuitable for normalisation. This study is the first systematic analysis of candidate reference genes inG. littoralisand will facilitate further investigation of normalisation of gene expression inG. littoralis.