The oleaginous yeast Yarrowia lipolytica is an important industrial microorganism used for the production of lipids, proteins and various chemicals. The design of effective biotechnological processes with this cell factory requires an in-depth knowledge of its metabolism. Here we present a transcriptomic study of Y. lipolytica grown in the presence of two important carbon sources, namely glycerol and glucose, as well as in a mixture of both at different carbon to nitrogen ratios. It emerged that the transcriptomic landscape of Y. lipolytica is more sensitive to the nitrogen availability than to the utilized carbon source, as evidenced by more genes being differentially expressed in lower carbon to nitrogen ratio. In particular, expression of hexokinase (HXK1) is significantly susceptible to changes in nitrogen concentrations. Moreover, high HXK1 expression in low nitrogen seems to impact the expression of other genes which are implicated in tricarboxylic acid cycle and erythritol biosynthesis. We further show that expression of HXK1 and two genes belonging to the sugar porter family might be controlled by GATA-like zinc-finger proteins.