Alternative oxidase is a terminal oxidase in the branched mitochondrial electron transport chain of most fungi includingAspergillus niger(subgenus Circumdati, section Nigri). A second, paralogousaoxgene (aoxB) is extant in someA. nigerisolates but also present in two divergent species of the subgenus Nidulantes—A. calidoustusandA. implicatus—as well as inPenicillium swiecickii. Black aspergilli are cosmopolitan opportunistic fungi that can cause diverse mycoses and acute aspergillosis in immunocompromised individuals. Amongst the approximately 75 genome-sequencedA. nigerstrains,aoxBfeatures considerable sequence variation. Five mutations were identified that rationally affect transcription or function or terminally modify the gene product. One mutant allele that occurs in CBS 513.88 andA. nigerneotype strain CBS 554.65 involves a chromosomal deletion that removes exon 1 and intron 1 fromaoxB. AnotheraoxBallele results from retrotransposon integration. Three other alleles result from point mutations: a missense mutation of the start codon, a frameshift, and a nonsense mutation.A. nigerstrain ATCC 1015 has a full-lengthaoxBgene. TheA. niger sensu strictocomplex can thus be subdivided into six taxa according to extantaoxBallele, which may facilitate rapid and accurate identification of individual species