Eulemur mongoz is found in north-western Madagascar and in the Comoros on the islands of Moheli, Anjouan and Grande Comoro, where it was almost certainly introduced by humans. There might be a larger population of the species in Comoros than there is in Madagascar. On Madagascar, it is known from the region of Ambato-Boéni, including the Anaboazo, Ambahivahy, Mangidirano, Ankirihitra and Mariarano forests, and Ankarafantsika; the northern limit of its distribution appears to be near Analalava on the Bay of Narindra, and it has been seen south and west of the Betsiboka River at Katsepy and on the shores of Lac Kinkony, on both sides of the Mahavavy River and in the Tsiombikibo forest near Mitsinjo (Mittermeier et al. 2010). It ranges from sea level to 400 m. It is sympatric with E. fulvus north of the Betsiboka River, and with E. rufus south of it. Mongoose Lemurs have sometimes been observed intermingling with E. fulvus groups during feeding bouts, but usually keep to themselves and are much more cryptic than the latter species.

This species is likely affected by national trends in forest habitat loss: Madagascar lost 37% of its forest cover from 1973 to 2014, with an annual deforestation rate of 1.1%/year from 2010 to 2014. Almost half of Madagascar's forest (46%) is now located within less than 100 metres from the forest edge (Vieilledent et al. 2018).

This species is listed on Appendix I of CITES. It is protected by law in the Comoros. It is known to occur in the protected areas of Ankarafantsika National Park (Ampijoroa), the Mahavavy-Kinkony Wetland Complex (Anjamena, Analabe, Analamanitra, Ankamangoa, Bemahazaka, Tsilaiza, Anoloky, Tsimbokibo and Anoborengy) and Antrema at Katsepy (Mittermeier et al. 2010, Muller et al. 2000, Shrum 2008). More populations are being protected through community-based conservation of the Anaboazo, Ambahivahy, and Mangidirano forests in the Ambato Boeny District (H.L.L. Randrianarimanana/The Aspinall Foundation, unpublished reports), and in the future New Protected Area of Ankirihitra and Mariarano forests, where a community-based conservation programme is ongoing (Rakotondrabe and Razafindramanana 2019). The highest densities of the species are found in the Mahavavy-Kinkony Wetland Complex where high rates of deforestation are causing fragmentation within the already very small fragments. The species does not appear to move between fragments and seems limited to only the largest of the remaining forest patches (Shrum 2008). Attention is quickly needed toward the enforcement of the remaining large fragments within the Mahavavy-Kinkony Wetland Complex, as well as the forests surrounding Ambato-Boeny, as the last of the viable habitat for the species is quickly being further fragmented.