A total of 250 isofemale lines derived from Korean populations (Daekwanryeong, Seoul, Choenan, Taegu and Cheju) of Drosophila melanogaster were examined to find their status in respect to the hobo system of hybrid dysgenesis and the molecular structure of the hobo elements in their genomes. hobo activity was found to be extremely low in these populations (average, 0.9%). The average GD sterility percent was 2.5% in the cytotype test. The lines tested for GD sterility were characterized as H- (3.6%), H0 (80.0%), and H- (16.4%). The result of in situ hybridization analysis using 2.6 kb XhoI probe revealed that H-, H0, and H- strains had 35.8±3.1, 41.4±2.0 and 36.0±6.8 copies per genome, respectively. Included these copy numbers are 6.6±0.9, 7.8±2.2 and 5.0±1.2, hobo elements, respectively, showing hybridization with the 0.9kb EcoRI probe. It may indicate the presence of complete hobo elements. On the basis of Southern blot hybridization experiment using XhoI restriction enzyme, all the populations appeared to have a low copy number of 3.0 kb complete hobo elements and a high copy number of internally deleted hobo elements. the 1.5 and 1.7 kb potentially Th or Th-like elements, are preserved in all of these strains tested. Our results suggest that the presence of Th elements and other incomplete hobo elements provide explanation for the suppression of hobo-mediated hybrid dysgenesis in Korean populations of D. melanogaster.