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New zircon and apatite fission-track ages obtained on samples from all lithotectonic units exposed on Naxos Island are presented. Zircon ages of the exhumed metamorphic rocks range from 25.2 to 9.3 Ma and from 13.0 to 6.4 Ma for apatite. Zircon track-length analysis distinguishes partial overprinting of an earlier event (M1) in the south. Northwards no overprint is seen and the ages there represent rapid exhumation since c. 12 Ma. Both zircon and apatite ages are slightly older toward the north of the island probably due to variation of the geotherm in the proximity of the fault.

Zircon fission-track ages of the granodiorite range from 13.7 to 12.2 Ma are statistically identical to previously determined U–Pb ages. Apatite fission-track ages however, yield a younging trend from south to north from 12.9 to 9.0 Ma. This could be due to differential depth of emplacement and/or to differential exhumation during tectonic unroofing by a top-to-the north detachment.

Fission-track ages on detrital grains in Lower Miocene sediments indicate a source not identified within the present outcropping rocks of Naxos. Ages on boulders and grains in the Middle to Upper Miocene sediments point to rapid erosion until about 8.5–7 Ma.

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