Mutant populations generated by ethyl methanesulfonate (EMS) have been used for crop improvement and functional genomics. Since pepper is very recalcitrant to be transformed, EMS mutagenesis can be a very useful to generate useful alleles and to characterize the function of genes. We have been developing a mutant population aiming at 5,000 mutants by treating EMS on seeds of C. annuum ‘Yuwolcho’. A total of 4,300 M1 mutants have been developed until now. Among the 4,300 M1 population, almost 800 M2 mutant lines have been phenotyped and evaluated to confirm the effect of EMS. We categorized seven key organ development and subdivided them into twenty secondary categories. Among them, 50 and 72 families have been shown variations in plant growth and leaf development, respectively. In addition, we detected nucleotide variations using HRM analysis in eIF4E and putative aminotransferase genes. These results demonstrated that our mutant population can be very useful for study function of genes in near future.