Bacterial seed and boll rot is a newly emerging cotton disease in Pakistan. Twenty-one cotton varieties were screened to find resistance source against the disease. None of these was found to be resistant. Five cotton varieties (CIM-595, MK2, BT-986, BT-986 & SG-1) having 700-1400 Area under disease progress curve (AU-DPC) units were found to be moderately resistant to the disease. SLH-317, FH-942, BT-222, BT-666, MNH-457 ranging from 1401-1700 AUDPC units were moderately susceptible while MNH-456, SLH-336, 9811, FH-942, MNH-886 susceptible to boll rot. Seven varieties (FH-114, FH-113, BT-7, BT-212, SLH-BT-4, BT-212 and FH-941) were highly susceptible to bacterial seed and boll rot indicated by 2001-2300 AUDPC units.Biochemical tests identified bacterial isolates as Pantoea agglomerans. Different inoculation techniques were assessed for bacterial pathogenicity and symptoms of boll rot were only observed in needle punctured bolls. One, two and three weeks old bolls were mechanically inoculated by injecting bacterial suspension to evaluate the boll's age impact on disease severity. Maximum severity was observed in two weeks old bolls. Red cotton bugs (Dysdercus cingulatus) were fed on artificially inoculated diseased bolls and then transferred on healthy bolls. Diseased symptoms were noticed on healthy cotton bolls. Bacterial colonies were recovered and red cotton bug was confirmed as the disease-transmitting vector.