One major complications to the use of herbicides for weed control is the ability of plants to evolve herbicide resistance, rendering the herbicides ineffective against target plants. Out of 31 known herbicide modes of action, weeds have evolved resistance to 21. 268 plant species are known to have evolved herbicide resistance at least once. Herbicide resistance was first observed in 1957, and since has evolved repeatedly in weed species from 30 families across the globe. Weed resistance to herbicides has become a major concern in crop production worldwide. 
Resistance to herbicides is often attributed to overuse as well as the strong evolutionary pressure on the affected weeds. Three agricultural practices account for the evolutionary pressure upon weeds to evolve resistance: monoculture, neglecting non-herbicide weed control practices, and reliance on one herbicide for weed control. To minimize resistance, rotational programs of herbicide application, where herbicides with multiple modes of action are used, have been widely promoted. In particular, glyphosate resistance evolved rapidly in part because when glyphosate use first began, it was continuously and heavily relied upon for weed control. This caused incredibly strong selective pressure upon weeds, encouraging mutations conferring glyphosate resistance to persist and spread.
However, in 2015, an expansive study showed an increase in herbicide resistance as a result of rotation, and instead recommended mixing multiple herbicides for simultaneous application. As of 2023, the effectiveness of combining herbicides is also questioned, particularly in light of the rise of non-target site resistance.
Plants developed resistance to atrazine and to ALS-inhibitors relatively early, but more recently, glyphosate resistance has dramatically risen. Marestail is one weed that has developed glyphosate resistance. Glyphosate-resistant weeds are present in the vast majority of soybean, cotton and corn farms in some U.S. states. Weeds that can resist multiple other herbicides are spreading. Few new herbicides are near commercialization, and none with a molecular mode of action for which there is no resistance. Because most herbicides could not kill all weeds, farmers rotate crops and herbicides to stop the development of resistant weeds.
A 2008–2009 survey of 144 populations of waterhemp in 41 Missouri counties revealed glyphosate resistance in 69%. Weeds from some 500 sites throughout Iowa in 2011 and 2012 revealed glyphosate resistance in approximately 64% of waterhemp samples. As of 2023, 58 weed species have developed glyphosate resistance. Weeds resistant to multiple herbicides with completely different biological action modes are on the rise. In Missouri, 43% of waterhemp samples were resistant to two different herbicides; 6% resisted three; and 0.5% resisted four. In Iowa 89% of waterhemp samples resist two or more herbicides, 25% resist three, and 10% resist five.
As of 2023, Palmer amaranth with resistance to six different herbicide modes of action has emerged. Annual bluegrass collected from a golf course in the U.S. state of Tennessee was found in 2020 to be resistant to seven herbicides at once. Rigid ryegrass and annual bluegrass share the distinction of the species with confirmed resistance to the largest number of herbicide modes of action, both with confirmed resistance to 12 different modes of action; however, this number references how many forms of herbicide resistance are known to have emerged in the species at some point, not how many have been found simultaneously in a single plant.
In 2015, Monsanto released crop seed varieties resistant to both dicamba and glyphosate, allowing for use of a greater variety of herbicides on fields without harming the crops. By 2020, five years after the release of dicamba-resistant seed, the first example of dicamba-resistant Palmer amaranth was found in one location.