Thermophilic strain Bacillus species AA contains several site-specific endonucleases and three of them have been identified. BspAAI recognizes the sequence 5'-C down arrow TCGAG-3' and cleaves it after the first "C" forming 4-nucleotide 5'-ends and is an isoschizomer of XhoI. BspAAII recognizes the sequence 5'T down arrow CTAGA-3' and cleaves it after the first "T" forming 4-nucleotide 5'-ends and is an isoschizomer of XbaI. BspAAIII recognizes the sequence 5'-GGATCC-3' and is an isomer of BamHI. The optimal temperature and pH values are 42-48 degrees C and 7.0-8.0, respectively.