Archived measurements by the X-ray Telescope on board the ASCA satellite of the single runaway O9.5V star, ζ Ophiuchi, are analysed. The data set is unique as it covers just more than one full rotational period of the star. We report a clearly detected periodic X-ray flux variability with amplitude ~20% in the ASCA passband (0.5-10 keV). The detected period ~0d.77 possibly indicates a connection with the recurrence time (~0d.875 ± ~0d.167) of the discrete absorption components (DACs) in UV spectra of the star, thought to be due to the presence of large scale structures in the stellar wind modulated by rotation. We attribute the X-ray fluctuation with an uneven distribution of X-ray absorbing material. We also report that an analysis of similar ASCA observations of ζ Puppis failed to confirm earlier reported variability of X-rays from this star based on ROSAT observations