Morphological traits have served generations of biologists as a taxonomic indicator, and have been the main basis to delineate species for museum taxonomists for centuries. Widespread awareness of the importance of behavioural characters, such as vocalizations, has arisen much more recently, and the relative importance of these different traits in the speciation process remains poorly understood. To shed more light on the interplay between morphological and behavioral traits in the speciation process, we generated a draft genome of a cryptic Southeast Asian songbird, the Limestone Wren-babbler Napothera crispifrons, and re-sequenced whole genomes of multiple individuals of all three traditional subspecies and a distinct leucistic population that had previously been misinterpreted as a plumage polymorphism. We demonstrate strong genomic and mitochondrial divergence among all three taxa, pointing to the existence of three species-level lineages. Despite its great phenotypic distinctness, the leucistic population was characterized by shallow genomic differentiation from its neighbor, with only a few localized regions emerging as highly-diverged. Quantitative bioacoustic analysis across multiple traits revealed deep differences especially between the two taxa characterized by limited plumage differentiation. Our study demonstrates that speciation in these furtive songbirds is not governed by the evolution of marked color differences, but is regulated by an interplay between color and bioacoustic traits. Extreme color differences can be anchored in few genomic loci and may therefore arise and subside rapidly.