Bacterial blight disease on cotton crop caused by the bacterial pathogen Xanthomonas axonopodis pv. malvacearum (Xam) is a serious disease found to infect both the transgenic (with Bt gene) and non-transgenic cotton varieties grown in the Western Vidharbha region of Maharashtra state, India. Different races of the Xam pathogen exist in the infected cotton crop. Their knowledge can be useful in breeding cotton varieties resistant to these races for the region. Similarly, the knowledge of the sensitivity of these Xam races to the various pesticides is useful in chemical disease management programs. At least 4 races of Xam were isolated from both transgenic (Bt) and non-transgenic cotton crops grown in this region. These races included race-7, race-29, race-30, and race-32 of the Xam pathogen. Further, the race-29 was differentiated into pathotype-A and pathotype-B based on their differential reaction on additional two differential cotton cvs viz. Gregg and DPX₄. This is the first report of the presence of pathotypes in Xam race-29. This is also the first report on how to differentiate the pathotypes in Xam race-29. No pathotypes in other Xam races were detected by using these two differentials. Transgenic and non-transgenic cotton crop varieties vary in their susceptibility (based on diseased water-soaking (WS) reaction, or resistant hypersensitive (HR) reaction) to these Xam races. Further, these races vary in their virulence (time required for the production of diseased reaction) on the same cotton genotypes. The infection phenomenon of Bt and non-Bt versions of cotton varieties was observed to be Xam- race specific. These Xam races did not differ in their sensitivity to a given pesticide. Antibiotics and a copper group of fungicides were effective in checking the growth of these Xam races under in vitro testing. The formation of pesticide-resistant mutants was not observed in these Xam races in this region.  Cotton crop varieties (Bt transgenic and their non-Bt version) resistant to these races have to be bred for cultivation in this region to minimize the losses due to this disease.