DNA Barcoding, Mostly Sanger sequencing and microsatellite genotyping are used in managing insect pest specially play important role for selection of correct biopesticides
DNA barcoding is helpful in proper identification of a particular species. Sequencing and microsatellite genotyping can reveal some gene sequences. Microsatellites can be used as markers in genetic studies of linkage in families and linkage disequilibrium studies of populations. So, if you got any marker for identification that can be useful in managing that particular species.
The IAEA pest management bulletin put out a special issue on this very topic, I think in January 2016. It would be worthwhile to check it out. It will tell you the current status of the Tephritid and Drosopilid pest groups.