Climate variability influences genetic and phenotypic diversity within species, impacting biodiversity’s evolution. Gene flow and selection maintain changes in genetic and phenotypic variants along an environmental gradient. We investigated a hybrid zone in western Ecuador, involving two wren species (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus, and their admixed populations. We addressed two primary questions: (1) What is the relative contribution of Isolation by Distance (IBD) and Isolation by Environment (IBE) to genetic differentiation in these species along the western Ecuadorian environmental gradient? (2) Is there evidence of genetic admixture and introgression between these taxa in western Ecuador? We analyzed 4,409 SNPs from 112 blood samples sequenced using ddRadSeq. Clusters ranged from K=2-4, aligning with geographic origins, known phylogenetics, and physical or ecological constraints. IBD was evident across all models, while IBE was less pronounced but still significant for annual mean precipitation and precipitation seasonality. Genetic admixture between C. f. pallescens and C. zonatus gradually changed along the environmental gradient. Genetic differentiation in the two C. f. pallescens populations could be attributed to an unreported potential physical barrier in central western Ecuador. The proximity of the Andes to the coastline restricted lowland habitats, limiting dispersal and gene flow, especially among dry-habitat specialists. Taxonomic changes are not proposed, but the admixture in C. f. pallescens suggests it may be a hybrid between C. z. brevirostris and C. fasciatus, with varying degrees of admixture in western Ecuador and northwestern Peru. This study enhances our understanding of avian population genomics in tropical regions.