Knowledge of the age and compositional architecture of Archean cratonic lithosphere is critical for models of geodynamics and continental growth on early Earth, but can be difficult to unravel from the exposed geology. We report the occurrence of numerous >3.7 Ga zircon crystals in 3.45 Ga rhyolites of the eastern Pilbara Craton (Western Australia), which preserve evidence for an Eoarchean meta-igneous component in the deep Pilbara crust. This inherited zircon population shares similar and distinctive age and Hf-O isotope characteristics with the oldest gneissic components of the Yilgarn Craton ∼500 km farther south, suggesting a common ca. 3.75 Ga felsic crustal nucleus to these two Archean granite-greenstone terranes. We infer a pivotal role for such ‘seeds’ in facilitating the growth and persistence of Archean continental lithosphere.