Destruxins, cyclic hexadepsipeptide toxins, secreted by the entomopathogenic fungus, Metarhizium anisopliae through extracellular synthesis. The present study reports a new approach for the analysis of DTXs produced by the fungal strain Metarhizium anisoliae Tk6, using FRIR-HPLC-LC-MS and H1 NMR. The results also showed that production of the major DTXs A, B, C, and E have to be determined in Czapek Dextrose (CD) liquid culture filtrate from 9 to 12 days post-inoculation. Purified DTX were further tested in bioassays to assess their effects of Aedes aegypti mosquitoes. The four major purified DTX compounds were found to cause a toxic effect on the larval developmental stages of mosquitoes with high mortality rates. However, DTX E outperformed the other three DTXs by causing the highest mortality three days after inoculation. This result gives an alternative approach of using DTXs in mosquitoes control and used as a new method for other pest management.