A combination of large-scale cultivation of highly susceptible cultivars and mild winters caused severe yield losses due to yellow rust in NW Europe in the early 1990s, but in recent years the disease has become less predominant. Several atypical Puccinia striiformis f. sp. tritici pathotypes have been observed in recent years, showing virulence spectra which made them able only to infect cultivars covering less than 5% of the wheat and triticale area in Denmark. Some were even unable to grow on any of the standard ‘European’ and ‘World’ yellow rust differentials. We observed 2 distinct groups of atypical pathotypes, each subdividing into 2 highly divergent AFLP phenotypes. It was striking that AFLP diversity among unusual pathotypes, sampled within a short time period in a small area on very few host cultivars, which induced limited or no selection on the pathogen population, was 3–4 times higher than among isolates sampled from a large number of cultivars with different Yr-genes in 4 different countries during more than 25 years. The repeated occurrence of atypical phenotypes of diverse origin may suggest a more frequent and even more distant dispersal of P. striiformis uredospores than previously anticipated. Finally, the disease reactions conferred by these unusual types on a wide range of differentials were used to discuss the limits for a genetic interpretation in terms of assessment of virulence and avirulence in pathogen isolates.