Certain phytopathogenic fungi are able to express alternative NADH- and quinol-oxidising enzymes that are insensitive to inhibitors of the mitochondrial respiratory Complexes I and III. To assess the extent to which such enzymes confer tolerance to respiration-targeted fungicides, an understanding of mitochondrial electron transfer in these species is required. An isolation procedure has been developed which results in intact, active and coupled mitochondria from the wheat pathogen Septoria tritici, as evidenced by morphological and kinetic data. Exogenous NADH, succinate and malate/glutamate are readily oxidised, the latter activity being only partly (approx. 70%) sensitive to rotenone. Of particular importance was the finding that azoxystrobin (a strobilurin fungicide) potently inhibits fungal respiration at the level of Complex III. In some S. tritici strains investigated, a small but significant part of the respiratory activity (approx. 10%) is insensitive to antimycin A and azoxystrobin. Such resistant activity is sensitive to octyl gallate, a specific inhibitor of the plant alternative oxidase. This enzyme, however, could not be detected immunologically. On the basis of the above findings, a conceptual mitochondrial electron transfer chain is presented. Data are discussed in terms of developmental and environmental regulation of the composition of this chain.