Direct sightings of Daubentonia madagascariensis are rare; its presence is often assumed from tree hole marks or feeding trace. Abundance is also hard to estimate, as one individual can make numerous feeding traces in search of insect grubs in dead and live wood trees and bamboo (Randimbiharinirina et al. 2017, Sefczek et al. 2017, 2019).  Furthermore, the nocturnal Aye-aye is quite adaptable and is known from a variety of habitats including primary rain forest, deciduous forest, secondary growth, dry scrub forest, and mangrove swamps. The species has also been noted to occur in cultivated areas, which are considered marginal, unsuitable, habitats. However, these plantations can support multiple individuals if there is adjacent endemic forest as well (Randimbiharinirina et al. 2017). The southern spiny desert appears to be the only habitat in which the species does not occur. Its presence in many areas appears to be determined largely by its primary food resource, the seeds of ramy (Canarium spp.) although there are also other dietary staples (Randimbiharinirina et al. 2017). During the day, D. madagascariensis sleeps in nests, tree forks or vine tangles. Nests may be occupied for a few days at a time and several individuals may use the same nest at different times (usually a female with a dependent offspring).  

Daubentonia madagascariensis has vast home ranges which exceed 600 ha; interestingly, individuals appear to spend more time moving along the ground than any other lemur except Lemur catta (Sterling 1993). Recent evidence suggests that Aye-ayes are not strictly solitary, but also forage in tandem and may exhibit differing relationships between animals of the same sex (Sterling and Richard 1995). Aye-ayes appear to have no restricted mating season (i.e. non-seasonal). A single offspring is born which is nurtured for 18 – 24 months before it is weaned. Females begin breeding at three or four years, and indications are that females give birth every two to three years (Petter and Peyrieras 1970, E. E. Louis, Jr. pers. comm.).

This species is listed on Appendix I of CITES. Daubentonia madagascariensis is reported to occur in numerous protected areas, including 13 national parks (Andohahela, Andringitra, Mananara-Nord, Mantadia, Marojejy, Masoala, Midongy du Sud, Montagne d' Ambre, Ranomafana, Sahamalaza-Iles Radama, Tsingy de Bemaraha, Tsingy de Namoroka, and Zahamena), seven strict nature reserves (Betampona, Tsaratanana, Makira, Farankaraina, Itampolo, Tsingy de Bemaraha, and Zahamena), and 14 special reserves (Ambatovaky, Analamazaotra, Analamerana, Anjanaharibe-Sud, Ankarana, Bora, Beanka, Forêt d' Ambre, Kalambatritra, Manombo, Manongarivo, Marotandrano, Nosy Mangabe, and Pic d' Ivohibe). They are found as well in the forests of Daraina (part of the Loky-Manambato Protected Area), as well as in the Maroala and Anjiamanginana Protected Forest, Kianjavato (part of the CO-FAV), Montagne des Français Protected Area and Torotorofotsy Ramsar Site. Yet despite occurring in a great many protected areas, their presence is often based only on signs and infrequent sightings, so there is little understanding of population size and dynamics until recently (review included citations). However, there is an urgent need for a systematic census of this important flagship species throughout its range, with the ultimate objective of developing a conservation action plan for the species. As of 2019, there were approximately 50 aye-ayes in various zoological collections worldwide (ZIMS 2019). There is a captive breeding programme involving various institutions, and an EEP and a SSP. This species has not successfully bred in second generation in captivity. Furthermore, due to their secretive lifestyle in the forest canopy without being directly observed, any ability to recognize crisis situation involving this species will most likely only noted after they have been extirpated from a location. Further efforts using molecular techniques to determine genetic health parameters and population dynamics and densities need to be pursued (Aylward et al. 2018).