Stress response of an organism is important for its survival. In responses to abiotic stresses such as heat, oxidative stress and nutrient limitations yeast cells activates trehalose biosynthesis and accumulates trehalose as stress protectant agent. Glycogen is also accumulated within the yeast cells as reserve carbohydrates. Trehalose and glycogen metabolism are well characterized in S. cerevisiae, but there is a limited information on these carbohydrates in candida species. In this study, we have analyzed the stress-dependent accumulation patterns of trehalose and glycogen in C. albicans as a pathogenic yeast and C. rugosa as an industrial yeast. Our results indicate that there are clear differences in storage carbohydrate metabolism between these two yeasts species. Basal levels of glycogen in C. rugosa 62 Hülya Karaca Gençer et al. is higher than the C. albicans glycogen content when these yeasts grown in normal conditions. However, when these yeasts subjected to stress inducing conditions, both trehalose and glycogen biosynthesis activated and rapidly accumulated within these yeast cells. Nonetheless, stress dependent activation of trehalose and glycogen biosynthesis in C. rugosa is much higher than the C. albicans. In addition, exposure of these yeast species to different abiotic stresses also resulted in activation of TPS1 and GSY1 gene transcription. The differences in trehalose biosynthesis and TPS1 transcript levels indicates that reserve carbohydrate metabolism is differentially regulated in C albicans and C. rugosa.