Diatoms, classified as photosynthesizing algae with siliceous skeleton frustules, can be found most in any aquatic habitat on earth, including fresh or coastal lakes, wetlands and almost everywhere humid. They can be classified in nine major classes which are Araphid, Eunotioid, Centric, Epithemioid, Monoraphid, Nitzschioid, Surirelloid, Asymmetrical Biraphid and Symmetrical Biraphid. Diatoms have precise ecological requirements, so they can also be sued as environmental indicators, it is telling us what is happening in the environment. The cell walls of diatoms may be preserved for long periods of time in sediments and provide a record of past changes in lake systems. This research aim is to identify the morphology of diatoms in lakes and reservoirs in USIM. The samples were collected by taking 250 ml of water from each lakes and reservoirs. Then, two drops of water sample were put on a cover slip and two drops of iodine were added. The samples were then observed under microscope and diatoms were identified by analyzing the types of morphology. Diatoms of symmetrical morphology were found in major lakes and reservoirs in USIM. The search for diatoms of other morphologies are still in progress. The morphology of diatoms can help us to know the water condition whether it is polluted or not. Therefore, this research is vital in environmental science as to provide information and support in the investigation to know the water condition.