The selection of Septoria tritici biotypes by Bobwhite’S’ resistant wheat germplasm was studied. Seedlings of cultivars with Bobwhite’S’ germplasm and with dwarf-mexican germplasm were inoculated in the greenhouse. Two Septoria tritici isolates (atypical yeast-like variant coming from Bobwhite’S’ germplasm and stromatic from traditional argentine germplasm) were used. Isolates of S. triciti from each isolate x cultivar combination were analyzed, and the percentage of regular or variant colonies was registered. Significant pathogen population effect and cultivar effect were demonstrated. The regular isolate produced chlorotic and necrotic lesions with pycnidia in all the cultivar; the atypical variant had quite distinct reaction according to the cultivars, being predominant the non-pycnidial necrotic reaction. Pathogen population isolated from Bobwhite’S’ germplasm produced higher levels of variant colonies, than did population isolated from dwarf mexican cultivar. Inoculation with the variant produced a high number of variant colonies in cultivars with both germplasm, indicating that Bobwhite’S’ germplasm could induce the origin of less pathogenic variants from a heterogeneous pathogen population through a remarkable mechanism of selective effect and any genetic change.