A disk drive is disclosed comprising a head actuated over a disk, and a spindle motor operable to rotate the disk. A bootstrap spiral track is written to the disk, wherein the bootstrap spiral track comprises a high frequency signal interrupted by sync marks. A first sync mark is written while writing a first part of the bootstrap spiral track, and a second sync mark is written while writing a second part of the bootstrap spiral track. A switch between writing the first sync mark and the second sync mark is made in response to a spindle BEMF voltage, thereby generating a sync mark seam in the bootstrap spiral track.