The cotton bollworm, Helicoverpa armigera is one of the most polyphagous and cosmopolitan pest species in world wide including Korea. It also showed high level of resistance against various types of insecticide. To set the integrated resistant management program, first, we tried to identify the insecticide resistant mechanism via transcriptome analysis of coding and non-coding RNAs using 4 strains (Australian susceptible and resistant strains, Korean and Brazilian resistant strains, additional a sub-lethal dose insecticide treatment in Korean resistant strain). From the illumina based RNAseq data sets with genome information, some resistant involved detoxification genes and long non-coding RNAs were discovered. Second, following molecular markers were developed from resistant strain specific amino acid substitution from those candidate genes. Third, functionally identified genes’ markers were applied in field populations using some molecular diagnostic tools such as LAMP (loop mediated isothermal amplification). Now additional functional analysis is going on for these un-characterized candidate genes and long non-coding RNAs.