The objective of this study was to compare the differences in ruminal fermentation and the proportion of rumen bacteria between swamp buffalo and cattle in the Philippines. Six crossbred swamp buffalo and six crossbred cattle used in the study were fed the same diet for 16 weeks. Rumen fluid was collected at weeks 0, 8, and 16 of the fattening period. Diversity of the rumen bacteria was analyzed using 454 pyrosequencing. The population density of major cellulolytic bacteria was determined by real-time PCR. Animal performance was not significantly different between buffalo and cattle. The concentration of total short chain fatty acids was found to be higher in the buffalo than in the cattle; however, the proportions of each short chain fatty acid were not significantly different. The proportion of Bacteroidetes increased in buffalo during the sampling period, whereas it was constant in cattle. In contrast, the proportion of Firmicutes and Fibrobacteres decreased in both groups of animals throughout the experiment. Although the density of cellulolytic bacteria between the two groups of animals was not found to be significantly different, the proportion of cellulolytic bacteria decreased during the fattening period. Both animal species exhibited similar traits for composition and population change of bacteria during the fattening period, suggesting that the microbial community structure might be dependent on feed rather than animal species.