Two populations of Palmer amaranth suspected of being resistant to glyphosate have been reported since 2007 in pecan orchards in Doña Ana County, New Mexico. The objectives of the study were to confirm and evaluate the level of resistance, to evaluate the effectiveness of alternative herbicide mechanisms of action, and to compare the cost of effective alternative herbicides for weed management in pecan orchards. Greenhouse experiments indicated that the resistant populations were able to survive glyphosate at 736 g ae ha−1. Compared with a susceptible (S) population, one of the resistant (R) populations had sevenfold resistance to glyphosate. POST application of 12 herbicides, with five different mechanisms of action, all provided at least 88% control of both R and S populations when applied at their recommended field rates. PRE application of trifluralin and metolachlor also provided more than 99% control of R and S populations. The results of field studies indicated that the financial benefit of season-long weed management with glyphosate, in pecan orchards, was comparable with some of the tested alternative herbicides.