Kinesin-1-powered microtubules have emerged as versatile components in biocomputing and biosensing technologies. However, the inability to identify and track individual microtubules has constrained their applications to ensemble behaviors, limiting their potential for single-entity-based nanotechnologies. To address this challenge, we present a novel method for encoding digital information directly onto individual microtubules using photobleaching patterns. Binary numbers (1 to 15) were encoded within ∼12 μm segments of moving microtubules by photobleaching with a stationary pulsed laser, creating spatial frequency patterns corresponding to distinct bits of information. Fourier analysis enabled the accurate retrieval of the encoded data, demonstrating the feasibility of direct information storage and retrieval on macromolecular structures. This approach offers a transformative solution for recording microtubule trajectories within nanotechnological devices by encoding path information directly onto microtubules at branch points, obviating the need for video-based tracking. We anticipate that this innovation will advance the development of individualized microtubule-based technologies.