This study presents a high-resolution record of Cu and Zn isotopes in four Fe-Mn crusts from the North and South Pacific oceans. North Pacific crusts were collected on the Apuupuu seamount south of the Hawaiian archipelago and South Pacific crusts were recovered near Rurutu Island in the Tahiti archipelago. Major and trace element compositions suggest that Cu and Zn in these crusts is of hydrogenous origin, i.e., precipitated from seawater, and they may therefore mirror deep seawater metal isotope. We show that Cu and Zn display different isotopic patterns between the North and the South Pacific Oceans but show similar temporal evolution within each geographical area. Copper and Zn isotope composition of both North Pacific crusts vary between 0.57 ‰ to 0.73 ‰ for δ65/63CuNIST976 and 0.97 ‰ to 1.25 ‰ for δ66/64ZnJMC-Lyon. In contrast, South Pacific crusts show resolvable temporal variations, with Cu and Zn isotopic ratios increasing sharply over the last ∼ 6 Ma from 0.16 ‰ to 0.51 ‰ and 0.67 ‰ to 1.09 ‰ respectively. Notably, we observed a positive correlation between δ65/63CuNIST976 and δ66/64ZnJMC-Lyon values in Fe-Mn crusts from the South Pacific. The correlation suggests mixing between two components in Fe-Mn crusts, a hydrothermal component with δ65/63CuNIST976 ∼ 0.2 ‰ and δ66/64ZnJMC-Lyon ∼ 0.7 ‰, and a Pacific deep seawater component with δ65/63CuNIST976 ∼ 0.7 ‰ and δ66/64ZnJMC-Lyon ∼ 1.2 ‰. These values are fractionated from modern dissolved Cu and Zn by a factor of −0.3 ‰ and 0.5 ‰ respectively. We suggest that the deep Southern Pacific Ocean received sustained hydrothermal input during the last 6 Ma, which was recorded in the Cu and Zn isotope composition of Fe-Mn crusts precipitated thousands of kilometers away. Our study highlights that hydrothermal venting may be a significant source of Cu and Zn in the deep oceans despite their extensive precipitation within hydrothermal vent fields. We show that this source could be persistent through time, and thus, it could have a significant impact on the biogeochemical cycling of Cu and Zn in seawater which would ultimately be recorded by Fe-Mn crusts.