Stem canker is a damaging disease of winter oilseed rape, caused by ascomycetous fungi Leptosphaeria maculans and L. biglobosa. The initial source of plant infection is ascospores, formed in pseudothecia on stubble from the previous growing season. The aim of this work was to evaluate the effectiveness of fungicide treatments at different times of application in the autumn on quality and quantity of seed yield, in relation to the concentration of ascospores of L. maculans and L. biglobosa in the air. Field experiments were done in Lower Silesia, the region of intensive oilseed rape cultivation, located in south-west Poland. We have demonstrated that, in case of high disease pressure, fungicide treatment against stem canker was most efficient when done 4-11 days after the highest concentration of pathogen ascospores in air. The seed yield, oil and protein content increased by 17.7-18.8 %, 1.60-1.72 % and 0.8-0.9 % respectively. In low disease pressure the optimal spray time was more flexible, but the highest yield was always following the maximum ascospore release. In some cases it also coincided with the increase of oil, without adverse effect on protein content. Furthermore, it coincided with the increase of indole glucosinolates, such as glucobrassicine and 4-hydroxyglucobrassicine, and -besides one studied year -it was also connected with decreased amounts of alkenyl glucosinolates. Both Leptosphaeria species were present in air and in infected plants during their vegetation. The ratio between both species depended on seasons; L. maculans prevailed on leaves in the autumn, whereas L. biglobosa dominated on stems before harvest.