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Considerable attention has been directed to studying the infection dynamics of the fungal pathogenBatrachochytrium dendrobatidis(Bd) affecting amphibians in the high elevations of the Neotropics. However, lowland forests of the same realm remain comparatively understudied in this context. Herein, we attempt to bridge this gap by measuring the prevalence ofBdvia quantitative polymerase chain reaction (qPCR) in several anuran taxa inhabiting the Amazonian lowlands in the northeast of Ecuador. To this end, we sampled 207 anurans from 10 different families, 25 different genera, and 55 distinct host species originally collected in 2008. Taxonomy (at the family level), morphology (i.e. weight and snout-vent length), and life-long aquatic dependency of hosts (i.e. aquatic index) were also compiled to serve as potential predictors ofBdinfection status. Our findings revealed a relatively highBdprevalence of 58%, with 88% of sampled anuran families testing positive for the fungus at varying proportions. Model selection involving fitting and testing several different linear models, including mixed linear models, revealed a significant negative relationship between host weight andBdinfection status (p < 0.01). However, no significant associations were observed between taxonomy, aquatic dependency, snout-vent length, andBdinfections. In addition, we only detected the global panzootic lineage ofBd(Bd-GPL) and not theBd-Asia-2/Bd-Brazil lineage via qPCR single nucleotide polymorphism (SNP) genotyping. Our findings contribute to the understanding ofBddynamics in the Neotropical lowlands and emphasize the need for future research on the ecological factors influencingBdin the Amazon and their implications for amphibian conservation.