Xylose is the second most abundant monomeric sugar on earth. Nevertheless, metabolizing xylose into ethanol is a complex process due to several biochemical reactions. Some microorganisms of the genus Mucor are suitable for this bioprocess. Using metal ions, such as zinc and calcium, allows some fungal species to increase their ethanol yield. In this work, the wild strain Mucor spp. (C1502) was molecularly identified via internal transcribed spacer (ITS) sequencing. Secondly, an optimization using response surface methodology (RSM) with a central composite experimental design (CCD) was carried out. The independent variables (X) were ZnSO4·7H2O (X1, 0.0−1.5 g/L) and CaCl2 (X2, 0.0−2.5 g/L) concentration in the fermentation broth in order to demonstrate the effect of these ions, xylose was used as the only carbon source. The dependent variables (Y) measured were ethanol yield (Y1, g ethanol/g xylose) and xylitol yield (Y2, g xylitol/g xylose). The identified strain, Mucor circinelloides, was given the accession number MN128960 by the NCBI. Once the optimal concentrations of zinc and calcium were calculated, experimental validation was performed, with the highest ethanol and xylitol yields reaching 0.36 g ethanol/g xylose and 0.35 g xylitol/g xylose, respectively. This study demonstrated that increasing the xylitol yield using the effect of the ions, zinc and calcium, increases the ethanol yield. Furthermore, M. circinelloides (C1502) can produce metabolites, such as ethanol and xylitol, from the xylose obtained from hemicellulose biomasses, which can be used as a carbon source at low cost and with great availability.