The evolution of weeds in USA agroecosystems predates herbicide tolerant (HT) crops by several decades. However, given the unprecedented adoption of genetically engineered (GE) HT crops, particularly in maize, cotton and soybean and the concomitant use of glyphosate, the evolution of glyphosate-resistant (GR) biotypes of agronomic important weeds now represents a significant threat to the sustainability of the GE HT trait and the herbicide. Notably, GR biotypes of horseweed (Conyza canadensis), common waterhemp (Amaranthus tuberculatus), Palmer pigweed (Amaranthus palmeri), giant ragweed (Ambrosia trifida) and johnsongrass (Sorghum halepense) have increased dramatically in frequency in conjunction with the adoption of crop production systems based on GE HT crops. Furthermore, other shifts in weed communities have been observed. It must be emphasized that the GE HT crops did not directly cause these weed shifts. The industry was responsible initially for these changes in weed communities given their initial positions that the glyphosate-resistant weed problems were unlikely to evolve and the recommendations to use glyphosate exclusively for weed management. However, decisions by growers to use glyphosate must be factored in as imparting selection pressure on the weed communities resulting in weed management problems, particularly when university recommendations strongly suggested not to use glyphosate in this manner. The key is now to provide growers with sufficient information to convince them to adopt integrated weed management programs and utilize best management practices. Given the presumed and real benefits of convenience and simplicity of the GE HT crop production systems; this will be a difficult task.