Bacillus thuringiensis is an aerobic endospore-forming bacterium that lives in the caterpillars of some moths and butterflies. It seems that it is the same organism as Bacillus cereus, a soil bacterium, and Bacillus anthracis, the cause of anthrax; the three organisms only differ in their plasmids.

Bacillus thuringiensis produces toxin crystals that are lethal to the caterpillars, but considered harmless to most other organisms, including humans. Therefore, the bacterium and its toxin are used in crop protection, especially in organic farming, where the use of chemical pesticides is not considered an option. This is done by spraying plants with the bacterium itself, or with an insecticide that contains the bacterial spores.

Another way to protect plants is to create transgenic plants that carry the gene for the bacterial toxin, as is currently done in the USA, India, China and Australia for cotton (Bt-cotton), and for corn (Bt-corn) in USA and Canada. This has generated some controversy, especially regarding the ill effects Bt corn was purported to have on the monarch butterfly.

There are strains of Bt that are effective against other insect larvae. Bt israelensis is effective against mosquito larvae and some midges.