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The chytrid fungus Batrachochytrium dendrobatidis (Bd) is a threat to the survival of amphibians worldwide, a situation that is compounded by several other factors. In this study, we determined the prevalence of Bd and its relationship to biotic and abiotic variables for six amphibian communities in two cloud forest fragments and four coffee agroecosystems in central Veracruz, Mexico. A sampling effort of 768 person-hours and 109 skin swabs resulted in the detection of B. dendrobatidis in four amphibian species belonging to three families. The co-inertia model showed the following as the most important variables: tree density, fern species, temperature and elevation, fragment or site size, and structural index. Conversely, we did not find a clear relationship between Bd prevalence and the habitat management gradient. The highest prevalence was found in the second cloud forest, but a very similar result was found in one of the traditional agroecosystems; the lowest levels of prevalence were found in another second traditional agroecosystem and the first cloud forest. The degree of infection was highest in the cloud forests where the diversity of trees, orchids, and elevation was higher. Ecnomiohyla miotympanum was the most abundant species and was found to be infected in four of the five sites, presenting the highest degree of infection.