Unique DNA-promoted Pd nanocrystals on carbon nanotubes (Pd/DNA–CNTs) are synthesized for the first time, in which through its regularly arranged PO43− groups on the sugar–phosphate backbone, DNA directs the growth of ultrasmall Pd nanocrytals with an average size of 3.4 nm uniformly distributed on CNTs. The Pd/DNA–CNT catalyst shows much more efficient electrocatalytic activity towards oxygen reduction reaction (ORR) with a much more positive onset potential, higher catalytic current density and better stability than other Pd-based catalysts including Pd nanocrystals on carbon nanotubes (Pd/CNTs) without the use of DNA and commercial Pd/C catalyst. In addition, the Pd/DNA–CNTs catalyst provides high methanol tolerance. The high electrocatalytic performance is mainly contributed by the ultrasmall Pd nanocrystal particles grown directed by DNA to enhance the mass transport rate and to improve the utilization of the Pd catalyst. This work may demonstrate a universal approach to fabricate other superior metal nanocrystal catalysts with DNA promotion for broad applications in energy systems and sensing devices.