The New World screw-worm (NWS), Cochliomyia hominivorax (Coquerel), is one of the most important parasitic insect pests that cause invasive myiasis in warm-blooded vertebrates. Because of the substantial economic losses to livestock rearing caused by this pest throughout the neotropics, an international effort has been involved in a program to eradicate the NWS from endemic areas of Central and South America and to prevent invasions into screw-worm-free areas. It is crucial to characterize the genetic variability of target populations in order to maximize the effectiveness of the eradication program. Ten polymorphic microsatellite loci previously isolated from an enriched library constructed for C. hominivorax are currently being used to investigate the genetic variability and population structure across its current geographic distribution. Preliminary results obtained from Uruguayan populations indicated a considerably high genetic variability. Statistical analysis indicated that most of the genetic variation is contained within populations, while low levels of differentiation were found between them. The investigation into the genetic variability and population structure of NWS from Central and South American populations should provide fundamental information for future eradication strategies.