E. pisi was thought to be the only causal agent of powdery mildew in peas, with three genes, er1, er2 and Er3, conferring resistance to this pathogen. Recently, E. trifolii has also been found to cause this disease in peas in different countries, but its relevance in pea powdery mildew disease worldwide is unknown. The objective of this study was to develop a method to identify and quantify E. pisi and E. trifolii and use it to analyze the relative prevalence of E. pisi and E. trifolii in pea fields in Spain and Tunisia. We also wanted to discern the effect of the er1, er2 and Er3 resistance genes on the relative amount of E. pisi/E. trifolii. Using the polymorphic sites present between E. pisi and E. trifolii ITS sequences, we developed a qPCR method capable of identifying and quantifying these pathogens. Our results revealed, for the first time, the occurrence of E. trifolii in Tunisia and that the presence of er1, er2 and Er3 genes have a clear effect on the ratio E. pisi/E. trifolii in both countries.