The Late Palaeozoic rocks of southern Portugal have a complex thermal history. Vitrinite reflectance determinations from 90 samples confirm that the organic maturity of Late Palaeozoic rocks in SW Portugal is very high, mainly corresponding to meta-anthracite coal rank. The optic fabric of vitrinite in oriented coal samples from the Brejeira Formation suggests maturation under simple, non-tectonic, burial conditions with peak temperatures being attained prior to Variscan deformation. The lack of any increase in vitrinite reflectance with depth through c. 1 km of section in borehole AC-1 is not consistent with conductive heat transfer and is interpreted as the result of late synorogenic to post-orogenic advective heating. This heating episode generated temperatures sufficiently high to produce levels of maturity corresponding to meta-anthracite coal rank through much of the terrane now exposed, but not high enough to result in overprinting of the pre-deformation optic fabric of vitrinite in the thin coals. The slightly lower maturity of older, platform-facies rocks in the Aljezur–Bordeira area may reflect either deposition on a basement high followed by less burial than adjacent parts of the basin, or the area being the site of a sink for descending relatively cool fluids.