The filamentous fungus Alternaria alternata is a potent producer of many secondary metabolites， some of which like alternariol or alternariol-methyl ether are toxic and/or cancerogenic. Many Alternaria species do not only cause post-harvest losses of food and feed， but are aggressive plant pathogens. Despite the great economic importance and the large number of research groups working with the fungus， the molecular toolbox is rather underdeveloped. Gene deletions often result in heterokaryotic strains and therefore， gene-function analyses are rather tedious. In addition， A. alternata lacks a sexual cycle and classical genetic approaches cannot be combined with molecular biological methods. Here， we show that CRISPR/Cas9 can be efficiently used for gene inactivation. Two genes of the melanin biosynthesis pathway， pksA and brm2， were chosen as targets. Several white mutants were obtained after several rounds of strain purification through protoplast regeneration or spore inoculation. Mutation of the genes was due to deletions from 1bp to 1.5kbp. The CRISPR/Cas9 system was also used to inactivate the orotidine-5-phosphate decarboxylase gene pyrG to create a uracil-auxotrophic strain. The strain was counter-selected with fluor-orotic acid and could be re-transformed with pyrG from Aspergillus fumigatus and pyr-4 from Neurospora crassa. In order to test the functioning of GFP， the fluorescent protein was fused to a nuclear localization signal derived from the StuA transcription factor of Aspergillus nidulans. After transformation bright nuclei were visible.