The photosynthetic apparatus is dually inherited with components being contributed by both the nuclear and cytoplasmic genomes, which must function together for photosynthesis to be efficient. The objective of the present study is to determine if the replacement of the cultivated tetraploid cotton cytoplasm (AD2) with alien ones affects photosynthesis and other gas exchange parameters. Ten different alloplasmic lines with cytoplasms A2, B1, C1, D2-2, D3-d, D8, E1, AD1, AD2 and AD5 in 57-4 nuclear background (AD2) were grown in field plots with three replications. Leaf photosynthetic rate (PN), stomatal conductance (COND), intercellular CO2 concentration (Ci), transpiration rate (E) and water use efficiency (WUE) were determined at four different sampling dates from July 25 to August 19. Alloplasmic lines with wild diploid cytoplasms had 7.2 to 24.3% higher PN than 57-4, with a mean of 11.3%, while the cytoplasms from A2, AD1 and AD5 had less effect on PN (5% higher than 57-4). The exotic cytoplasms, especially wild ones, had markedly positive effects on COND of water, but generally had no significant effect on Ci, E and WUE. The positive effects of exotic cytoplasms on PN and COND did not persist over the last sampling date. There were significant correlations among PN, COND and E.