New transgenic cotton (Gossypium hirsutum L.) technologies Bollgard II/Roundup Ready Flex (BGII/RRF) provide additional mechanisms for the cotton crop to retain early initiated fruiting structures positioned in the lower canopy. It may be possible, therefore, for early fruit retention to become too high with these new technologies resulting in early cutout and reduced yield. The objective of this investigation was to determine if glyphosate-induced differences in early season retention occur between BGII/RRF and the older Bollgard/Roundup Ready (BG/RR) technologies and if so, to test if these differences in retention impact crop maturity, yield, or quality under irrigated and nonirrigated conditions. A study was conducted in 2004 and 2005 at two locations in southwestern Georgia to compare the two technologies under dryland vs. irrigation with or without flower removal. The BG/RR matured later than BGII/RRF when glyphosate was applied late at the seventh and 11th leaf stages. The BG/RR compensated for fruit loss by producing heavier remaining bolls. The BGII/RRF maturity was unaffected by the late glyphosate applications and produced a higher percentage of plants having a harvestable boll in the lower canopy than BG/RR. The BGII/RRF cotton had increased boll number and weight at the first sympodial position at lower main stem nodes while BG/RR produced more and heavier bolls on upper main stem nodes. Flower removal did not negatively affect BGII/RRF or BG/RR yields. Few differences in fiber quality were observed. The BGII/RRF retained more early reproductive structures than BG/RR but also cutout earlier. Yield differences between the two technologies may be due to agronomic performance of the variety backgrounds used.