Microbial contamination is one of the most common causes of deterioration and quality loss in foods. Dairy products provide a suitable environment for microorganism multiplication. Yogurts are products that usually suffer from the action of yeasts, which are frequently associated to packaging swelling. The yogurt’s productive process was monitored for 18 weeks in a dairy product and, once a week, three samples of 100g were collected from the produced flavor. One of the samples was analyzed at time zero while the other two were stored in two environments: one was refrigerated at 10°C and the other was stored at 22°C. Once yeast presence was detected, the proceeding step was the identification by the API20C AUX commercial kit, followed by the characterization through scanning electron microscopy. At high storage temperatures (22°C), simulating what might occur during product distribution and commercialization, the yeast population increased concomitantly to the increase of lactic acid bacteria number and packaging swelling. Yeast population was lower on the early manufacturing days. Two species were identified: Kluyveromyces marxianus and Saccharomyces cerevisiae, which were compared by their morphologies and dimensions, presenting similarities between them. Isolated yeasts are considered safe by the FDA. Results have shown that temperature is one of the most essential factors to assure quality to the finished product.