The buffy-tufted-ear marmoset (Callithrix aurita) is a small primate endemic to the Brazilian Atlantic Forest biome, and one of the 25 most endangered primates in the world, due to fragmentation, loss of habitat, and invasion by allochthonous Callithrix species. Using occurrence data for C. aurita from published data papers, we employed model selection and cumulative AICc weight (w+) to evaluate whether fragment size, distance to fragments with allochthonous species, altitude, connectivity, and surrounding matrices influence the occurrence of C. aurita within its distributional range. Distance to fragments with C. jacchus (w+ = 0.94) and non-vegetated areas (w+ = 0.59) correlated negatively with C. aurita occurrence. Conversely, the percentage of agriculture and pasture mosaic (w+ = 0.61) and the percentage of savanna formation (w+ = 0.59) in the surrounding matrix correlated positively with C. aurita occurrence. The findings indicate that C. aurita is isolated in forest fragments surrounded by potentially inhospitable matrices, along with the proximity of a more generalist and invasive species, thereby increasing the possibility of introgressive hybridization. The findings also highlighted the importance of landscape factors and allochthonous congeneric species for C. aurita conservation, besides indicating urgency for allochthonous species management. Finally, the approach used here can be applied to improve conservation studies of other endangered species, such as C. flaviceps, which is also endemic to the Brazilian Atlantic Forest and faces the same challenges.