Frankenia thymifolia Desf. is an endemic plant of North Africa found in saline habitats. The ethyl acetate extract of its dried roots was subjected to silica gel column chromatography, leading to the isolation of three compounds: a new sulphated lignan (pinoresinol 4-sulfate, compound 1), a new naphthalene derivative (1,2,3,4,5,7-hexamethoxynaphthalene, compound 2), and a known phenolic derivative (4,5-dimethoxy-3-hydroxybenzoic acid methyl ester, compound 3). Their structures were established using one- and two-dimensional NMR spectroscopy (COSY, HSQC, HMBC) and mass spectrometry (ESI-MS, HRESIMS). Compound 1 is the first naturally occurring pinoresinol sulfate, and compound 2 is the first reported natural hexamethoxynaphthalene. This study confirms that plants of the genus Frankenia can synthesize sulfated compounds, which is correlated with their preference for saline environments and serves as an indirect chemotaxonomic marker for the genus.