Local Omani chickens, although well adapted to the climatic conditions of the Sultanate of Oman are poor performance when compared to breeds such as the Cobb 500 broiler chickens. Two experiments were conducted to compare the growth performance and the composition of intestinal microflora between local Omani and Cobb500 broiler chickens maintained under an intensive management system. The main objective of the first experiment was to compare the growth performance of local Omani and Cobb500 broiler chickens raised under intensive management system. One hundred and eighty birds of local Omani and Cobb500 broiler chickens were divided into two groups with fifteen replicates, each replicate containing six birds. The birds were fed a non- medicated conventional corn-soybean meal diet. Feed intake, body weight gain, and feed conversion ratio were recorded weekly. At the end of the growth experiment period (35 days), fifteen birds per breed were randomly selected for morphological analysis of the jejunum and ileum, carcass and organs weight. Blood was collected for hematological and serum biochemistry analysis. Hematological and serum analysis showed that there was no significant difference between Omani and Cobb 500 broiler suggesting that the birds are healthy. Morphological analysis showed that Cobb 500 broiler had greater villi height compared to the Omani breed (P<0.01) and subsequently a significantly higher feed intake (63.8%), significantly higher body weight gains (72.1%) better feed conversion ratios than the Omani breed (1.50 vs 1.96). However, local Omani chicken have significantly heavier relative organ weights (p<0,001) In the second experiment, 16S rDNA-based analysis was employed to explore the effect non-medicated conventional corn-soybean meal diet on the bacterial communities in the gastrointestinal tract of the two breeds of chickens. This study showed that optimal development of the small intestinal is associated with a preponderance of Bacilli (98%) in the duodenum at Day 5 of Cobb500 chickens and that the inferior growth rate of the local Omani chickens was assumed to be related to the smaller number of Bacilli (68.5%) in their Duodenum at Day 5. The large number (25.8%) of the fermenting bacteria, Clostridia in the duodenum at Day5 in the local Omani chickens versus 0.88% in the duodenum of the Cobb500 was postulated to be associated with inferior development of the small intestine and subsequently, inferior nutrient digestion and absorption.