Scedosporium and Pseudallescheria fungi are increasingly encountered fungal pathogens. Species identification is important as there are differences in epidemiology, virulence, and antifungal susceptibility that vary according to species or species groups. Histological and culture techniques are limited by low sensitivity and specificity but improved culture approaches employing selective media have improved the recovery of these fungi from clinical samples. Molecular- and proteomics-based methods are increasingly explored and used for species identification. These include multiplex polymerase chain reaction (PCR) and other PCR-based methods, oligonucleotide arrays, DNA sequencing, rolling circle amplification, and matrix-assisted laser desorption time-of-flight mass spectrometry. These techniques have been harnessed for the detection and identification of Scedosporium and Pseudallescheria species directly from clinical samples and from cultures. This review summarizes the methods currently used to enable an informed choice of detection and/or identification techniques in the clinical mycology laboratory.