Aedes aegypti and Aedes albopictus are the major dengue vectors in Sri Lanka. A thorough understanding of the vector population is of paramount importance to develop effective strategies for combating the disease. Pattern of genetic diversity of Aedes aegypti and Aedes albopictus were examined by analyzing Ribosomal DNA (r-DNA) variations. 70 individual mosquitoes from 6 populations of Aedes aegypti and 70 individual mosquitoes from 5 populations of Aedes albopictus were analyzed for ITS2 based variations. A significant polymorphism was found even among mosquitoes caught from the same locality. Based on the results obtained both species could be divided into 2 major groups.