Antheraea mylitta is an endemic insect species producing the world famous tasar silk. Its populations occupying different ecological and geographical regions show certain degree of phenotypic variability for which they are known as 'eco-races'. In order to understand the genetic variability and phylogenetic relationship among the different eco-races we characterized a repetitive TaqI genomic DNA fragment as a genetic marker. The sequence analysis and Southern hybridization show the repetitive nature of TaqI DNA fragment, designated as A. mylitta TaqI family repeat, AmTFR. The PCR amplification of AmTFR reveals its presence in all the tested eco-races of tasar silkworm and some other silk producing insects. The AmTFR is evenly distributed in all 31 meiotic metaphase I chromosomes as observed by fluorescent in situ hybridization. The AmTFR based phylogenetic analysis of the eco-races is not congruent with the morphological variations and their geographical distribution.