BACKGROUND: Effectors are critical in the antagonistic interactions between plants and pathogens. However, knowledge of mutation mechanisms and evolutionary processes of effectors remains fragmented despite its importance for the sustainable management of plant diseases. Here, we used a population genetic approach to explore the evolution of the effector gene Pi04314 in Phytophthora infestans, the causal agent of potato blight. RESULTS: We found that Pi04314 gene exhibits a low genetic variation generated by point mutations mainly occurring in the signal peptide. Two of the 14 amino acid isoforms completely abolished the secretion functions of signal peptides. The effector is under purifying selection, supported by the comparative analyses between its population differentiation with that of SSR marker loci as well as by negative Tajima's D (-1.578, p = 0.040) and Fu's FS (-10.485, p = 0.000). Furthermore, we found that the nucleotide diversity of Pi04314 is significantly correlated with the annual mean temperature at the collection sites. CONCLUSION: These results suggest that the evolution of effector genes could be influenced by local air temperature and signal peptides may contribute to the ecological adaptation of pathogens. The implications of these results for agricultural and natural sustainability are discussed.