Aims: This work aims to determine the factors which play a role in establishing the microbial population throughout the digestive tract in ruminants and is necessary to enhance our understanding of microbial establishment and activity. Methods and Results: This study used Terminal Restriction Fragment Length Polymorphism (TRFLP) to investigate the microbial profiles of 11 regions of the digestive tract of two breeds of sheep (Beulah and Suffolk). TRFLP data revealed that the regions of the digestive tract were highly significantly different in terms of the composition of the bacterial communities within three distinct clusters of bacterial colonization (foregut, midgut and hindgut). The data also show that breed was a significant factor in the establishment of the bacterial component of the microbial community, but that no difference was detected between ciliated protozoal populations. Conclusions: We infer that not only are the different regions of the tract important in determining the composition of the microbial communities in the sheep, but so too is the breed of the animal. Significance and Impact of the Study: This is the first time that a difference has been detected in the digestive microbial population of two different breeds of sheep.