Marine invertebrate borings are very rare in crystalline rocks, providing evidence of particular strategies producers use to colonise these unfavourable substrates. In the Sorbas Basin (Almería, southern Spain), Upper Miocene transgressive successions contain blocks of metamorphic and igneous rocks of the Nevado–Filabride Complex of the Betic Cordillera. Ichnological analysis of the embedded blocks shows the presence of two types of macroborings located in gneiss boulders, revealed to be an extraordinary case worldwide. The most abundant are regular hemispherical depressions ascribed reservedly to the well-known, mostly bivalve boring Gastrochaenolites. The second one is a pouch-like depression, tapering downward, elliptical in outline, and clearly different to other non-circular-in-outline, pouch-shaped macroborings. Thus, a new ichnogenus and ichnospecies Cuenulites sorbasensis has been defined. According to the overall shape, an endolithic or semi-endolithic bivalve using chemical means to bore is suggested as the tracemaker. Colonisation could be determined by sea-level coastal dynamics, with decreasing energy during advancing transgression allowing boring, which was then stopped due to supply of fine-grained sediment that killed the borers.