PCR and molecular hybridization provide new methods to detect microorganisms in environment. A simple, sensitive protocol was developed to detect Bacillus thuringiensis HD-1 in soil by PCR and Southern Blotting in this study. Methods of extracting DNA from soil and purification were compared. By a modified total DNA extraction from soil and purification, followed by PCR and Southern Blotting, strain HD-1 released into soil can be detected with a sensitivity of 2.2 x 10(2) cells/g soil. By using other specific primers, this detection protocol can be widely used in the research of ecology and risk assessment of genetically engineered microorganisms released into environment.