Moniliophthora perniciosa (Marasmiaceae) causes witches' broom, one of the most important fungal diseases of cacao in the Americas. In this study, we evaluated the in vitro characteristics and the population dynamics of the pathogen in the Peruvian Upper Amazon, center of diversity and domestication of the crop. We collected fifty samples from six cacao growing districts: three with more intensive cacao cultivation and closer to urban areas, and three where cacao plots are more dispersed and are managed by people in native communities in remote Amazonian areas. All samples were isolated in pure culture and their macro and micro characteristics were evaluated. Isolates were also molecularly genotyped with an eleven microsatellite-marker. We identified nine morphological patterns of mycelial growth, which were related to the abundance or scarcity of clamp connection-bearing hyphae and culture growth rate, and had no relation with their origin. Conversely, the microsatellite genotyping revealed that the population genetics and dynamics of the pathogen in the region is shaped by the intensity of cacao cultivation. Districts with more intensive cacao plots had a reduced diversity (Shannon index, H = 0.69–1.10) compared to remote districts deeper into the Amazon (H = 1.10–2.30). Additionally, clustering, and minimum spanning network analyses revealed that all genotypes in the districts with more intensive cultivation derived from the genotypes in remote districts, i.e., the pathogen was introduced from areas located deeper into the Amazon. Moniliophthora perniciosa was first observed in the Brazilian Amazon in the 1780's and it spread to Bahia, the main cacao cultivation region of this country, not before 1989. Our findings reveal a similar pattern in the invasive history of M. perniciosa in Peru. Keywords: Escoba de bruja, genetic diversity, molecular genotyping, witches' broom disease