Balancing the flexibility and stability of behavior is a fundamental aspect of neural function, underlying both normal motor function and its disruption in neurodegenerative diseases like Parkinson's and Huntington's diseases. The study of song in songbirds, a learned and highly quantifiable motor skill, has been instrumental in uncovering the neural principles underlying both the maintenance and plasticity of behavior. In particular, the Bengalese finch (Lonchura striata domestica), a domesticated estrildid finch derived from the white-rumped munia (Lonchura striata), exhibits substantial variability and plasticity in the ordering and spectral content of its song elements. This natural behavioral variability and capacity for change provides a powerful experimental framework that can be leveraged to understand the molecular factors that facilitate and restrict neural plasticity.To establish a platform for the molecular analysis of song variability and plasticity, we have generated an initial draft assembly of the Bengalese finch genome from a single male animal to 143x coverage and an N50 of 3.0 MB. Furthermore, we have developed an initial set of gene models using RNA-seq data from eight samples that comprise liver, muscle, cerebellum, brainstem/midbrain, as well as, forebrain tissue from juvenile and adult Bengalese finches of both sexes.In addition to providing a valuable resource for efforts to characterize the molecular mechanisms underlying behavior, these data will add to the growing collection of assembled avian genomes. Moreover, Bengalese finch laboratory populations possess substantial phenotypic and genetic diversity, on the order of outbred human populations, which allows genetic linkage analysis for a range of quantitative characteristics, from plumage to specific song features. Furthermore, these data combined with a future genomic characterization of the white-rumped munia will provide a distinct resource to examine the molecular events underlying recent domestication.