A sapphire, zircon and magnetite-bearing xenolith from Khao Wua, near Chanthaburi in Thailand, conclusively demonstrates a common origin for the sapphire, zircon and magnetite found in alluvial deposits in the Chanthaburi gem fields. The original aluminium- and titanium-rich octahedral magnetite crystal in the xenolith exsolved into hercynite, magnetite and hematite during cooling. It includes minor anhedral jarosite–alunite, possibly originating as an iron-sulphide-rich immiscible liquid. Uranium-lead isotope dating of zircon in the xenolith gives an age of 1–2 (± <1) million years (Ma). This falls within fission track ages for alluvial zircons (2.57 ± 0.20 Ma) from the Chanthaburi—Trat gem fields and within the potassium-argon ages of 0.44 to 3.0 Ma for the alkali basaltic volcanism in the Chanthaburi Province. These data suggest a common origin for sapphire, zircon and magnetite, and link them with the processes involved in alkali basaltic magma generation. The high iron and zirconium, low magnesium, and the inferred sulphides suggest pegmatite-like crystallization in an incompatible-element enriched, silica-poor magma (partial melt or fractionation product) in the deep crust or upper mantle. Etch features on exposed surfaces of the xenolith indicate that it was transported out of its equilibrium environment by the rise of later magma.