Amphibians at the global scale are dramatically declining and the pathogenic fungus Batrachochytrium dendrobatidis (Bd) has been suggested to be an important driver in this biodiversity crisis. Increasing evidence points towards the global emergence of Bd being a panzootic caused by pathogen pollution. Africa has been suggested to be the origin of the pathogen but remains one of the least-studied areas. We have conducted the most comprehensive survey on the continent to date focusing on Kenya for investigating taxonomic and environmental components in the distribution of Bd in tropical Africa. Eleven sites along a 770 km transect from the coast up to the border of Uganda were surveyed. Using quantitative PCR, we screened 861 samples from 23 different species in nine genera. The pathogen was confirmed at all studied sites, with an overall prevalence of 31.5%. No dead or symptomatic specimens were found and no declines have been reported in the region so far. Both prevalence and parasite load ranged from the detection limit to some of the highest ever reported. The parasite load showed a significant taxonomic bias and a strong inverse correlation with temperature. Our findings suggest that Bd may be enzootic in the region. We recommend that further research should focus on comparative experimental studies of susceptibility to Bd in African species. Moreover, we stress the need for improved knowledge on the conservation status of the tropical African amphibian fauna to confirm the enzootic nature of widespread Bd infections.