Basalts at mid-ocean ridges are generated by partial melting of the Earth’s upper mantle. As a result of this process, the upper mantle has become depleted over time in elements that are preferentially removed by melting. Although mid-ocean-ridge basalts have traditionally been thought to reflect the chemical composition of such depleted mantle, recent work has revealed the existence of domains in the upper mantle that are apparently not sampled by the basalts. Here we present the lead (Pb), neodymium (Nd) and hafnium (Hf) isotope compositions of peridotites from the Horoman orogenic massif in Japan, which is considered to represent the residues of melting of the upper mantle. These peridotites exhibit the lowest Pb isotope ratios reported from any known mantle material, along with high Nd and Hf isotope ratios. These data suggest that chemical depletion of the peridotites occurred around a thousand million years ago, and that they represent ancient mantle domains that have escaped convective stirring and homogenization. We suggest that such domains—if abundant in the mantle—may constitute a hitherto unrecognized reservoir with highly unradiogenic lead.