Song divergence among populations can theoretically lead to reproductive divergence and speciation. Despite many studies, this theory is still controversial. Habitat differences have been shown to shape songs, but few studies have looked for a link between ecologically driven acoustic and genetic divergence. We tested whether environmental selection has driven song divergence in two genetically distinct, but hybridizing, subspecies of the grey-breasted wood-wren (Henicorhina leucophrys) in Ecuador. Several acoustic features showed significant divergence between the subspecies. Spectral song divergence correlated with ambient noise profiles which differed significantly between the habitats of both subspecies. Temporal song divergence also corresponded as expected to vegetation density. However, in terms of quantified levels of reverberations, we found no significant differences in habitat-dependent sound transmission properties. We conclude that ecological niche segregation may explain acoustic divergence among the two wren subspecies. The resulting habitat-dependent song divergence may have contributed to reproductive divergence by guiding assortative mating in parapatric conditions or just currently contribute to maintenance of reproductive isolation upon secondary contact.