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Agricultural biotechnology aims to scrutinize the field crops which feed half of the world’s population by improving their agronomic traits using various biotechnological tools. Pea- an important cash crop, rich in nutrients, but frequently infected with powdery mildew (fungal disease caused by Erysiphe pisi) that destroys the whole crop and causes economic loss for growers. We, therefore, targeted this research to find the pathogen-resistant pea lines and further decipher the diversity at er locus among resistant pea lines. Screening for resistant pea lines was done with Erysiphe pisi isolates (Genebank submission: KX455922.1) under the net house and greenhouse conditions. Molecular studies revealed that the Erysiphe resistant (er1) gene was present in 40 lines out of selected 50 pea lines and the mutational character was conferred up to 36 genotypes with 11 haplotype groups. The haplotype (gene) diversity (Hd) was found to be 0.5571 ± 0.099 SD and the nucleotide diversity (Pi) was 0.0160 ± 0.0042 SD Majority of resistant lines (67%) occurred in Hap-1, other remaining haplotypes (Hap 2–10) having 33% resistant lines, each showing characteristic nucleotide substitutions with respect to reference PsMLO1 gene; genotypes from these divergent haplotypes can be used in pea resistance breeding to avoid genetic homogeneity and genetic vulnerability.