Thirteen bacterial biological control agents were applied as seed treatments in greenhouse experiments. The effects on colonization of cotton roots caused by application of fungicide seed treatments and residual acidity from delinting were determined. Seed treatments of metalaxyl, captan, carboxin, PCNB, and TCMTB (0.3 g a.i. / kg seed, 1.1 g a.i. / kg seed, 1.1 g a.i. / kg seed, 1.1 g a.i. / kg seed, and 0.08 g a.i./ kg seed, respectively) did not adversely affect colonization of roots after 14 days, though there were small increases in colonization of some strains and decreases in colonization of others. The ability of bacteria to grow on pesticide-amended agar was also determined. Captan and TCMTB reduced growth of all Bacillus spp. tested. In greenhouse studies, the low seed-surface pH (2.3) of commercial seed did not reduce root colonization when compared with colonization on roots from seed with a higher pH of 5.4. In field studies, colonization of two Bacillus subtilis strains (GB03 and GB07) was not significantly reduced by low seed-surface pH. These results indicate that bacterial strains can be combined with fungicides in integrated management systems, and the low seed-surface pH of acid-delinted cotton will not limit their application.