A correct identification of mold species causing human infections is of the utmost importance since treatment may differ depending on the infecting species. However, this is still a challenge in the current clinical practice, relying upon a morphological examination of a cultured isolate. In the first part of this PhD the focus was on Fusarium, a mold genus causing a wide variety of opportunistic human infections. In order to study the clinically relevant species diversity, the more than 300 Fusarium strains in the Belgian fungal culture collection BCCM/IHEM, mostly isolated from patients, were re-identified by multilocus DNA marker sequencing and phylogeny. The remaining 289 validated strains, comprising 40 different species, were of great value: (i) Analysis of the strain information revealed a species, i.e. Fusarium musae, of which it was not yet known that it caused human infections. (ii) A new species, closely related to Fusarium, was described, i.e. Pseudofusicolla biseptata. (iii) In vitro antifungal susceptibility testing was performed on the Fusarium dataset showing the importance of a correct species (complex) identification. (iv) The Fusarium dataset was used to prove the feasibility of the MALDI-TOF mass spectrometry identification as opposed to the, often difficult, morphological identification. In the second part of this PhD the focus was on the development of a new identification method for mold infections which is directly applicable on clinical samples and relies upon the detection of species- and genus-specific peptides using tandem mass spectrometry. Candidate peptides were selected according to a mass spectrometry based proteomics study. Accurate genus identification of Fusarium and species identification of Aspergillus BCCM/IHEM collection material was possible and the new method was optimized for the analysis of clinical samples.