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The nature of the protolith(s) of high-grade gneisses from the Aegean Cycladic Basement Unit of the islands of Paros and Serifos is investigated using whole-rock geochemistry and Sr–Nd–O isotopes, in order to better understand their origin and to compare with possible equivalents from the southern Aegean region. On Paros, the basement unit consists of heterogeneous, mylonitized upper amphibolite-grade paragneisses and associated migmatitic rocks, whereas on Serifos, it consists of a mylonitized felsic gneiss, intercalated with layers and lenses of S-type leucogranites and minor mafic metavolcanics. New Nd, Sr and O isotope data suggest a predominantly crustal-derived source in the gneiss protolith from both islands: high initial 87Sr/86Sr ratios (≥7052 to 0.711, calculated at 300 Ma), negative initial εNd (−2.8 to −7.7) values for bulk-rock gneiss samples, and high δ18O values of quartz separates (+10 to +12.7 ‰). Major and trace-element variations corroborate that chemical differentiation within the NW Paros gneiss subunit results from progressive migmatitization. Peraluminous gneisses from eastern Paros share clear similarities with metapelitic gneisses from the Naxos gneiss dome, in terms of their trace-element patterns, εNd (300) and O isotope characteristics. The mineral assemblage, the fine grain size (due to intense mylonitization), and the metaluminous affinity of the South Serifos grey quartzofeldpathic gneiss do not allow for an unambiguous interpretation for these undated rocks; however, a combination of geochemical parameters and tectonic discrimination diagrams indicates an immature siliciclastic (greywacke) protolith from a continental island arc setting. Sr–Nd isotopic systematics indicates an increasing lower crustal component in gneisses from NW Paros, which is closer to the migmatitic core of the Paros dome. The overall isotopic trend of the gneissic Cycladic Basement Unit on Paros is spatially correlated with that of the Naxos gneiss dome. © 2016, Springer-Verlag Berlin Heidelberg.