Agricultural production systems that reduce the use of in-crop herbicides could greatly reduce risks of environmental damage and the development of herbicide-resistant weeds. Few studies have investigated the long-term effects of in-crop herbicide omissions on weed seedbank community size and structure. A crop-rotation study was sampled 10 yr after a strictly annual rotation and an annual/perennial rotation were exposed to different in-crop herbicide omission treatments. In-crop herbicides were applied either in all annual crops (control), omitted from oats only, or omitted from both flax and oats. Seedbank densities were greatest when in-crop herbicides were omitted from flax and oats, and this treatment also reduced crop yield. Shannon-Wiener diversity differed among crops in the annual crop rotation and among herbicide omission treatments in the perennial rotation. Herbicide omissions changed the weed-community structure in flax and in wheat and canola crops in the annual rotation enough to warrant alternate control methods in some treatments. The magnitude of the effects on the seedbank parameters depended largely on the competitive ability of the crop in which herbicides were omitted. No yield response to omitting herbicides in oats indicated that standard weed management practices have reduced weed populations below yield-loss thresholds.