The gut microbiota is characterized by high population density, diversity, complexity of interactions, as well as influences the nutritional, physiological and immunological processes in the host animal. In this study, the effect of a hyperlipidic diet on the gut microbiota modulation associated with obesity and type II diabetes was investigated. Clone libraries of 16S rRNA gene were sequenced to identify differences and similarities in the gut microbiota of the obese and type II diabetes mice induced by high fat diet. The microbial community structure was analyzed by PCR-DGGE and sequencing techniques and the diversity of these gut microbiota was characterized by bioinformatic tools. The metabolic functions of the gut microbiota allowed correlate them to the respective obesity and type II diabetes. It was observed that gut microbiota induced by hyperlipidic diet contributes and aggravate the obesity and type II diabetes. The disturbance in the composition of the gut microbiota due to feeding promotes the proliferation of certain groups of bacteria that are able to take advantage of this type of nutrient. The increasing proportion of Firmicutes in gut microbiota appears to influence the development of obesity and type II diabetes in two ways. The first is to improve the ability to extract energy from food while the next occurs to contribute in the development of a subtle inflammation typical of obesity, which spreads throughout the body and interfere in the use of insulin, as seen in previous study.