With the aim developing useful tools for the elucidation of the carotenogenic pathway and the optimization of β-carotene production in Rhodotorula glutinis, the wild strain C2.5t1 and the β-carotene overproducing 400A15 and the albino 200A6 mutants were utilized. Comparative proteomic analyses of the three strains by 2D-DIGE, followed by tandem mass spectrometry of proteins that are more expressed in the 400A15 mutant, led to the identifications of 37 sequences associated to enzymes that have a role in the biosynthesis of acetyl CoA and in the production of β-carotene. The application of two multifactorial experimental designs to 400A15 showed that the fine tuning of the concentration of carbon and nitrogen sources and of oxygen availability determines a significant increase in the production of β-carotene in 400A15 in respect to the wild strain. Moreover, the development of a multi-parametric flow cytometry method allowed the real time monitoring of the production of β-carotene and of the physiological state of the cell in bench scale fermentations. In summary, although the proteomic data originated by this study will need to be integrated by genomic data to deepen current knowledge on the carotenogenic pathway in R. glutinis, the results here reported represent a further step towards a more complete understanding of a poorly characterized yeast and its biotechnological exploitation