The bollworm, Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae), is known to infest more than 182 plant species belonging to 47 families, of which 56 crops are classified as "heavily damaged". Published literature comprehended that so far only 47 SSRs are available for public use. Current study screened publically available 57,248 EST resources to characterize SSRs and used them for the population genetic studies in 60 collections of H. Armigera from chilli pepper, tomato, pigeon pea and cotton. We isolated 171 microsatellites, out of which 17 were di-nucleotide repeats (DNRs), 155 tri-nucleotide repeats (TNRs) and 5 tetra nucleotide repeats (TTNRs) of which 82% were located within the open reading frames, 10% in 5’UTRs and 8% in 3’UTRs. Present study revealed that the number of the SSRs are relatively lesser in lepidopteran insect genomes comparatively to the other insect families. Eighty six primer pairs were used to amplify 60 collections that resulted in 45 polymorphic primers. We annotated all the genes that contain SSRs using BLAST search. Genetic differentiation and gene flow among the intra and inter insect collections from pepper, tomato, pigeon pea and cotton were analysed using the AMOVA, population structure and mean frequency of private alleles. AMOVA revealed that the genetic differentiation within and among the groups is highly significant. Our study concluded that there is significant occurrence of gene flow among the insect collections from various crops. Allele numbers, PIC values, observed and expected heterozygosity, deviations from the Hardy-Weinberg equilibrium for various SSRs used in the study will be presented.