More selective than most chemical pesticides in that they ordinarily destroy only unwanted species, biocontrol agents (such as insects, fungi, and viruses) eat, infect, or parasitize targeted plant or animal pests. However, biocontrol agents can negatively affect nontarget species by, for example, competing with them for resources: a biocontrol agent might reduce the benefits conferred by a desirable animal species by consuming a plant on which the animal prefers to lay its eggs.

Another example of indirect negative consequences occurred in England when a virus introduced to control rabbits reduced the amount of open ground (because large rabbit populations reduce the ground cover), in turn reducing underground ant nests and triggering the extinction of a blue butterfly that had depended on the nests to shelter its offspring. The paucity of known extinctions or disruptions resulting from indirect interactions may reflect not the infrequency of such mishaps but rather the failure to look for or to detect them: most organisms likely to be adversely affected by indirect interactions are of little or no known commercial value and the events linking a biocontrol agent with an adverse effect are often unclear. Moreover, determining the potential risks of biocontrol agents before they are used is difficult, especially when a nonnative agent is introduced, because, unlike a chemical pesticide, a biocontrol agent may adapt in unpredictable ways, so that it can feed on or otherwise harm new hosts.