A patterned-media magnetic recording disk drive uses an optical system for accurately clocking the write data. The disk has concentric data tracks patterned into discrete magnetizable data islands with nonmagnetic spaces between the islands. As the disk rotates, a radiation source directs near-field radiation to the islands and spaces, and a radiation detector receives reflected radiation. The radiation is directed from the source through an optical channel or waveguide on the air-bearing slider that supports the read and write heads. The optical channel or waveguide has a near-field transducer at the disk-facing surface of the slider where the near-field radiation exits and reflected radiation returns. The reflected optical power varies depending on whether the near-field transducer couples to an island or a space, so the radiation detector output signal represents the frequency and phase of the islands as the disk rotates. The write clock that controls write pulses to the write head is responsive to the radiation detector output signal, so the frequency and phase of the write clock signal can be matched to the frequency and phase of the islands as the disk rotates.