Experiments conducted in 2003 to 2006 at the University of Arizona Maricopa and Safford Agricultural Centers (MAC and SAC) investigated weed management in RR Flex cotton and Liberty Link Cotton. Factors investigated included the type of pendimethalin application (preplant incorporated [PPI] or preemergence), method of cotton planting (dry planted or planted to moisture), rate and sequence of glyphosate or glufosinate applications, the method of post-directed spray application and the use of residual layby herbicides. The preplant incorporated use of pendimethalin provided excellent control of Palmer amaranth (AMAPA) and suppression of annual morningglory (IPOHE) in terms of both reduced weed density and slower growing weeds resulting in a longer early season postemergence herbicide application window and improved weed control. For example at MAC in 2005 at 34 DAP (days after planting), AMAPA plants were 6.8 cm tall with 8.8 leaves per plant and there were 205 plants m^-2 in the absence of pendimethalin compared to plants that were 2.5 cm tall with 6 leaves per plant with a density of 5.2 plants m^-2 in the presence of pendimethalin (1.1 kg ai/ha). Similarly, at 34 DAP, IPOHE plants were 4.8 cm tall with 4 leaves per plant and there were 48 plants m^-2 in the absence of pendimethalin compared to plants that were 2.0 cm tall with 2 leaves per plant and a density of 13.3 plants m^-2 in the presence of pendimethalin. The effects of pendimethalin on weed size resulted superior Palmer amaranth control after early season topical herbicide applications and in greater suppression of ivyleaf morningglory after two sequential postemergence herbicide applications. In Roundup Ready Flex cotton at 13 days after topically applying glyphosate (0.84 kg ae/ha), AMAPA control was 99% and 80% with and without PPI pendimethalin, respectively, and there was no difference in IPOHE control. Cotton plants averaged 8 nodes of growth in treatments with PPI pendimethalin but cotton plants in treatments without PPI pendimethalin only averaged 2 nodes of growth and were stunted 87%. At 24 days after post-directed glyphosate applications (1.26 kg ae/ha) that followed topical applications (0.84 kg ae/ha), AMAPA control was 99% and 81% with and without PPI pendimethalin, respectively, and IPOHE control was 91% and 83% with and without PPI pendimethalin, respectively. Cotton growth (i.e., height and number of nodes) was greater throughout the season and cotton yields were greater in weed control programs that included a preplant incorporated (PPI) pendemethalin application. The use of pendimethalin was especially critical in Liberty Link cotton; most treatments without PPI pendimethalin could not be harvested due to the presence of large pigweeds. In several studies, residual herbicide (e.g. prometryn) applied at layby was necessary to protect cotton yield and avoid having morningglory vines on top of the cotton canopy at harvest.