Molybdenum isotopes (reported as δ98Mo relative to NIST-3134) show resolvable isotope differences in igneous rocks with the continental crust being markedly heavier in isotope composition than mid-ocean ridge lavas, lunar basalts or the Earth’s mantle. The tholeiitic differentiation series at the intra-plate Hekla volcano (Iceland) shows no resolvable Mo isotope differences from basaltic to rhyolitic compositions. In contrast, convergent margin lavas show a transition from isotopically lighter mantle to heavy continental crust, suggesting that subduction processes drive continental crust towards heavier values. Archean komatiitic lavas, presumed probes of the Archean mantle, have Mo isotope values identical to modern depleted mantle, raising the questions if and how the Mo isotope crust-mantle disparity developed so early in Earth’s history. Here we present new Mo isotope data for a set of cumulate rocks from the Upper Zone of late Archean (2.8 Ga) Windimurra Igneous Complex, a mafic/ultramafic layered intrusion. The intrusion is not subduction related and contains no apparent primary hydrous minerals. We tested the effect of crystal fractionation on Mo isotopes in relatively dry melt along a tholeiitic liquid line of descent by using the cumulate effect of normally anhydrous minerals in the layered intrusion. Near mono-mineralic olivine-pyroxene-rich, feldspar-rich and Fe-Ti-rich oxides show small variations (~0.15‰) in Mo isotope signatures. This is consequently to predominantly isotopically light Fe-Ti-oxide-rich and isotopically heavier feldspar-rich rocks, respectively. This is suggesting minor Mo isotope fractionation, even in dry, tholeiitic systems, which however, counterbalance each other and thus potentially remain undetected. On average, the Windimurra mantle source is indistinguishable, or slightly isotopically lighter than the Mo isotope signature of komatiites. This is reinforcing an isotopically light Mo isotope signature of Archean mantle sources of high-degree mantle melts and is extending these signatures to predominantly mafic Archean crust. It remains to be tested if Archean felsic crust resembles modern continental crust in its heavy isotope values and to which extend the mantle was already isotopically depleted in Mo isotopes at Mesoarchean time.