Many populations of New Zealand plants and animals exhibit low densities, poor recruitment, fragmentation and high extinction risk caused by invasive mammals that established widespread dense populations after they were introduced. Conservation organizations invest in pest control to reduce levels of herbivory and predation on native biota, and use captive rearing and translocation to help the most endangered cases. Behavioural studies of brushtail possums, ship rats, house mice, stoats, ferrets, cats, goats, pigs, tahr and deer help to improve poison, trapping, hunting and fencing operations. Trained dogs are increasingly used to find pest animals that have survived control operations, and recreational hunters are required to train their dogs to avoid birds before they are granted access to some areas. Behavioural studies of rare birds, bats, lizards and invertebrates are done to identify the agents of decline, reduce the risks of pest control for their protection and increase the success in re-establishment of extirpated populations. Conservation work in terrestrial ecosystems is characterized by pragmatic problem-solving which means behavioural research tends to follow rather than lead innovations by wildlife managers. Behavioural studies of freshwater organisms have had a more theoretical orientation and have shown how introduced predatory fish can change the behaviour of native invertebrates. In marine ecosystems, researchers have quantified changes in cetacean behaviour caused by tourist encounters and by aquaculture. The challenges of studying animal behaviour in natural environments in New Zealand include: predator-prey interactions have not arisen over evolutionary time scales and no level of coexistence may be possible; breeding by some threatened or endangered taxa is not annual and may require episodic increases in food supply; mutualisms and interactions amongst native organisms were not described before they were disrupted by agents of decline; and some invasive mammals are valued hunting resources.