Information on the influence of water quality on the presence of bacteria under actual field conditions is limited. Most of the previous studies solely characterized the bacteria that were isolated whether from water, sediment or different fish organs, while lacking in determination of the associations of the environmental variables, especially water quality in influencing the presence of the bacteria. Under true field conditions, as experienced with real fish culture in natural water bodies, combinations of various environmental variables, especially from the water quality may influence the presence of bacteria (Arulampalam et al., 1998 and Vezzulli et al., 2002). Thus, this study was conducted in order to determine the associations between water quality and the presence of bacteria in cage cultured red hybrid tilapia, Oreochromis niloticus × O. mossambicus, in selected lakes and river in Peninsular Malaysia.