Just as it occurs between traditionally improved crops and wild relatives, pollen mediated gene flow occurs between GMCs and wild relatives or conspecifics despite all possible efforts to reduce it. Little is known about the long-term persistence of crop genes in wild populations or about the impact of fitness-related crop genes on the population dynamics of weedy relatives. The main concern with trangenes that confer significant biological advantages  is that they may transform wild/weed plants into new or worse weeds. In the cases of  hybridization of HRCs with populations of free living relatives will make these plants increasingly difficult to control, especially if they are already recognized as agricultural weeds and if they acquire resistance to widely used herbicides. Transgenic resistance to glufosinate is capable of introgressing from Brassica napus into populations of weedy Brassica napa, and to persist under natural conditions (Snow and Moran 1997). In Europe there is a major concern about the possibility of pollen transfer of herbicide tolerant genes from Brassica oilseeds to Brassica nigra and Sinapis arvensis (Goldberg 1992).

World-wide in 2000, transgenic herbicide resistant crops were planted on 74% of the 44.2 million hectares devoted to transgenic crops (James 2000). In North America, there are now commercially available transgenic glufosinate resistant cultivars of canola and corn, and transgenic glyphosate resistant cultivars of soybean, corn, cotton, and canola. Bromoxynil resistant transgenic cotton has also been developed. The so-called Round-up ready soybeans are the most prevalent GMCs.

Transgenic herbicide resistance in crop plants simplifies chemically based weed management because it typically involves compounds that are active on a very broad spectrum of weed species. Post-emergence application timing for these materials fits well with reduced or zero-tillage production methods, which can conserve soil and reduce fuel and tillage costs (Duke l996).

However, HRCs also have significant problems. Reliance on HRCs perpetuates the weed resistance problems and species shifts that are common to conventional herbicide based approaches. Herbicide resistance becomes more of a problem as the number of herbicide modes of action to which weeds are exposed becomes fewer and fewer, a trend that HRCs may exacerbate due to market forces. Given industry pressures to increase herbicide sales, acreage treated with broad-spectrum herbicides will expand, exacerbating the resistance problem. For example, it has been projected that the acreage treated with glyphosate will increase to nearly 150 million acres. Although glyphosate is considered less prone to weed resistance, the increased use of the herbicide will result in weed resistance, even if more slowly, as it has been already documented with Australian populations of annual ryegrass, quackgrass, birdsfoot trefoil and Cirsium arvense (Gill, 1995).

Perhaps the greatest problem of using HRCs to solve weed problems is that they steer efforts away from crop diversification and help to maintain cropping systems dominated by one or two annual species. Crop diversification can not only reduce the need for herbicides, but also improve soil and water quality, minimize requirements for synthetic nitrogen fertilizer, regulate insect pest and pathogen populations, increase crop yields, and reduce yield variance. Thus, to the extent that transgenic HRCs inhibit the adoption of diversified cropping systems that include rotational crops, cover crops and green manure, they hinder the development of sustainable agriculture.