This work presents a systematic study of zircon and apatite in melt-bearing impactites from the annular trough of the ~180 km and ~66.04 Ma Chicxulub impact crater, Yucatán, Mexico, using in situ laser ablation – inductively coupled plasma mass spectrometry, in which the petrologic context of the analysed minerals was assessed. Geochronologic U–Pb results for variably shocked zircon from the Yaxcopoil-1 core, including monocrystalline grains and neocrystallised granular aggregates, yielded a discordant array of ages representing the Early Palaeozoic age of the crystalline–metamorphic Maya block in the crater basement and the timing of the Chicxulub impact, respectively, and provide evidence for impact-induced resetting of the U–Pb system. Zircon and fluor-chlorapatite from the Yaxcopoil-1 core, and fluorapatite in clasts of impact melt from the Yucatán-6 core have low 206Pb/204Pb, suggesting the presence of detectable common Pb. The Chicxulub impactites were altered in an initially hot hydrothermal system that lasted up to ~2 Myr; locally, Pb-rich sulphides precipitated. Hydrothermal conditions did not reset the U–Th–Pb systematics of relict zircon, however, due to elevated closure temperatures for Pb diffusion at the fast cooling rates associated with the crater locations of the Yucatán-6 and Yaxcopoil-1 boreholes. Thus, the zircon preserves pre-impact and impact-related ages, rather than those of the hydrothermal system. In contrast, no useful geochronologic information was obtained from relict apatite, because common Pb in these grains overwhelmed radiometrically derived isotope ratios.