The cerambycid beetle Dectes texanus texanus LeConte, is an indigenous, univoltine species, which has established as a major pest of cultivated sunflower in the recent years. During 1970’s this species emerged as a new pest on soybean. Later, this pest has been recorded on soybean regularly over the time. However, it is not sure that whether the populations infesting sunflower and soybean are panmictic or isolated? A study on this aspect will help us in understanding the process of speciation and its effect on pest management. Therefore a study was initiated to understand its population biology. As a first step, we developed polymorphic microsatellite markers from genomic DNA enriched for microsatellite loci. A total of 10 polymorphic loci were identified. These loci were amplified across various populations of D. texanus collected from various counties in Kansas. Results of the study will help in understanding the structure, dispersal, genetic relationship and gene flow among the populations of soybean and sunflower. The markers developed for the study form an important tool to study the population genetics of Dectes stem borer and can also be used for the DNA finger printing studies.