The carnivores of Madagascar are likely the least studied of the world's carnivores, thus little is known about threats to their persistence. I provide the first long-term assessment of Madagascar's rainforest carnivore community, including: 1) how multiple forms of habitat degradation (i.e., fragmentation, exotic carnivores, human encroachment, and hunting) affect native and exotic carnivore occupancy; 2) how native and exotic carnivore temporal activity overlap and how body size and niche explain these patterns; 3) how native and exotic carnivores spatially co-occur across the landscape and which variables explain these relationships; and 4) how native and exotic carnivores and humans co-occur with lemurs across Madagascar's largest protected landscape: the Masoala-Makira landscape. From 2008 to 2013 I photographically sampled carnivores and conducted line-transect surveys of lemurs at seven study sites with varying degrees of degradation and human encroachment, including repeat surveys of two sites. As degradation increased, exotic carnivores showed increases in activity and occupancy while endemic carnivore, small mammal, and lemur occupancy and/or activity decreased. Wild/feral cats (Felis sp.) and dogs (Canis familiaris) had higher occupancy (0.37 ± SE 0.08 and 0.61 ± SE 0.07, respectively) than half of the endemic carnivore species across the landscape. Additionally, exotic carnivores had both direct and indirect negative effects on native carnivore occupancy. For example, spotted fanaloka (Fossa fossana) occupancy (0.70 ± SE 0.07) was negatively impacted by both wild/feral cat (beta = -2.65) and Indian civets (beta = -1.20). My results revealed intense pressure from hunting (ex. n = 31 fosa Cryptoprocta ferox consumed per year from 2005-2011 across four villages), including evidence that hunters target intact forest where native carnivore and lemur occupancy and/or activity are highest. I found evidence of high temporal overlap between native and exotic carnivores (ex. temporal overlap between brown-tail vontsira Salanoia concolor and dogs is 0.88), including fosa (Cryptoprocta ferox) avoiding dogs and humans across all seasons. However, I found no evidence of body size or correlates of ecological niche explaining temporal overlap among carnivores. Estimates of spatial co-occurrence among native and exotic carnivores in rainforest habitat revealed strong evidence that native and exotic carnivores occur together less often than expected and that exotic carnivores may be replacing native carnivores in forests close to human settlements. For example, falanouc show a strong increase in occupancy when dogs are absent (0.69 ± SE 0.11) compared to when they are present (0.23 ± SE 0.05). Finally, the two-species interaction occupancy models for carnivores and lemurs, revealed a higher number of interactions among species across contiguous forest where carnivore and lemur occupancy were highest. These various anthropogenic pressures and their effects on carnivore and lemur populations, particularly increases in exotic carnivores and hunting, have wide-ranging, global implications and demand effective management plans to target the influx of exotic carnivores and unsustainable hunting affecting carnivore and primate populations across Madagascar and worldwide. / Ph. D.