Emerging infectious diseases (EIDs) may indirectly influence community structure by altering biotic interactions in which affected species participate. This kind of indirect effects has received little attention to date, although recent research suggest they may not be infrequent. Chytridiomycosis is an EID that is affecting amphibian assemblages worldwide. Here we present the first (to our knowledge) field evidence of its indirect effect on assemblage structure through the disruption of a biotic interaction. We have documented an expansion of the common toad (Bufo bufo) after chytridiomycosis nearly extirpated the midwife toad (Alytes obstetricans) in Peñalara Natural Park (Central Spain). Bufo bufo has significantly increased its number of breeding sites. All newly occupied breeding ponds were colonized once the large numbers of large, overwintering A. obstetricans tadpoles they had previously held disappeared. An experiment demonstrated that breeding B. bufo adults strongly avoided laying eggs in water containing A. obstetricans tadpoles, accounting for observed patterns of pond use. A second experiment failed to show any predation by large A. obstetricans tadpoles on B. bufo eggs, but other researchers have documented reductions in condition, growth and survival of B. bufo larvae caused by the presence of A. obstetricans tadpoles. In Peñalara, chytridiomycosis attacks B. bufo too, but its effect on it has been quite less severe than on A. obstetricans. Our findings show how, besides any chytridiomycosis direct effects, interspecific differences in its impact may alter assemblage–influencing biotic interactions and, hence, assemblage structure in indirect ways.