The release of nitrogen compounds in water bodies causes serious environmental damage and one of its main sources are sewage. Nitrogen conventional processing is performed by bacteria called nitrifying in the presence of oxygen, and denitrifying in anoxic medium. This study aimed to determine the morphological characteristics of nitrifying microorganisms (bacteria oxidizing Ammonia - BOA and bacteria oxidizing nitrite - BON) and denitrifying (DESN) adhered in material support (MS) and suspension (Effluent - EF and Lodo- LD) in a fixed bed reactor treating domestic sewage under different cycles intermittent aeration (AI). They were worked three phases aeration and no aeration (EA / AN): Phase I 4h / 2h, Phase II 2h / 1h and Phase III 2h / 2h, using a hydraulic retention time of 16h. Samples of the MS, EF and LD were collected 2 times each AI cycle. The samples were inoculated in test tubes containing media specific for each bacterial group to confirm the presence or absence thereof. After 20 days of incubation for BOA and BON and 3 days for DESN tests were performed to verify the tubes that had positive results for each group. The positive tubes were removed about 0,1 mL of sample and inoculated from solid media (specific for each group) and incubated at 25⁰C. The characterization of Colony Forming Units - CFU of BOA, BON and DESN were performed visually based on data in the literature and morphotypes analysis of the isolated bacteria by Gram staining. After the cultivation was obtained 14 different colonies of BON, 9 of BOA and 25 DESN. The BON and DESN presented a number of similar colonies to EF, MS, and LD and colonies BOA were found in greater numbers in samples EF. As for the morphology and arrangement, bacteria Streptobacillus type were the most found in DESN also presenting Staphylococcus spp. and Streptococcus spp. less. The BOA were identified in greater quantity bacteria coco bacillus type. From the results it was concluded that the AI cycles worked not come to affect the diversity of organisms present in the analyzed media, bacterial colonies being viewed with the same characteristics in all cycles.