In February 2007, a European consortium, led by DSM Food Specialties publically released the A. niger (CBS 513.88) genome.

The genome sequence was obtained by the process of BAC walking, followed by shotgun sequencing of selected large BACs. The selected BACs (505 in total), representing the minimal tiling set covering the genome, had an average size of 76.8 kb and were sequenced with a coverage of 7.5x. Automated and manual annotation were carried out by the European Consortium. ORFs were automatically predicted by FGENESH (trained on A. niger and related organism sequences) as well as several other prediction programs. For all predicted ORFs, function and structure were predicted using PEDANT-ProTM software and then manually verified.

The genetic and phyiscal maps were established by using parasexual recombination and electro-phorectic karyotyping. There are eight chromosomes (I to VIII) within CADRE.