Olivine-rich lavas in the Margi area, Cyprus, are part of the boninitic Upper Pillow Lava series of the Troodos ophiolite. Re-Os isotope compositions of both whole rock and olivine phenocrysts of these lavas have been measured to determine the initial 187Os/188Os isotope compositions of the primary boninitic magma. The Margi lavas have high and variable whole rock Re-Os isotope compositions (187Re/188Os: 1.060–8.613; 187Os/188Os: 0.1307–0.1599), with (87Sr/88Sr)90Ma (0.705936 ± 0.001021), εNd(90 Ma) (5.6 ± 2.5), and δ18O (8.59 ± 0.38 ‰). In contrast, olivine phenocrysts, which host spinel and melt inclusions, have low and constant 187Os/188Os from 0.1301 to 0.1336 and low 187Re/188Os from 0.1350 to 1.557. Initial 187Os/188Os of these olivine phenocrysts (0.1300 ± 0.0041) is lower than that of whole rock (0.1373 ± 0.0135). These facts indicate that the olivine phenocrysts faithfully record initial 187Os/188Os of the primary boninitic magmas, which are comparable to the 187Os/188Os of primitive mantle, whereas whole rock Re-Os isotopes have been affected by secondary processes after olivine crystallization. Further geochemical modeling indicates that, although Os can be mobilized during slab dehydration, the contribution of crustal Os is insufficient to significantly raise the 187Os/188Os of the mantle wedge in a nascent subduction zone. Overall, our findings provide new insights about Os recycling in the early stages of subduction.