A procedure to extract genomic DNA from small insects of Blastophaga javana Hill (Hymenoptera: Agaoninae) and Ceratosolen solmsi marchali (Hymenoptera: Agaoninae) for PCR amplification is described. We compared the amplification of both cytochrome oxidase I (COI) gene and nuclear gene (Microsatellites) for specimens with different storage times in 95% ethanol. We found that with the modified protocol, a single, clean DNA fragment from the specimens can be amplified. The PCR amplifications from specimens with shorter storage times are much better. We found that the fragment that the microsatellite (SSR) amplified from B. javana is single and stable. This method is simple, reliable, economical, needs minimal equipment and reagents, and is important in addressing the difficulty of DNA extraction from a single very small insect.