Fungal contaminants may be health risk factors in general indoor and occupational environments. The identification of microfungi by macro- and micro-morphological characters is known to be very difficult and time consuming. An alternative method for identification of fungi using a molecular biological method based on a commercially available kit is described. The method is based on the DNA-extraction and subsequent amplification of the D2 expansion region of the large subunit of the fungal rDNA. DNA extraction, amplification, sequencing and database screening can be performed within 24 hours. A total of 28 different fungal species were identified on a morphological basis and compared with identification by the molecular biological method. The database comparison revealed identification down to the species for 12 samples and to the genus level of 11 samples. Five samples could not be identified. It is concluded that the identification of fungi by molecular biological method needs to be improved. This can partly be reached by expanding the fungal DNA-sequence datasets.