We investigated genomic divergence, interspecific and intraspecific diversity and population structure, local directional selection, and complex demographic history in a popular freshwater species complex in the Central Interior Highlands, North America. Specifically, we assessed differentiation between the Neosho Bass (Micropterus velox) and Smallmouth Bass (M. dolomieu) where their ranges are parapatric in this ecoregion. We scanned the genome for signatures of local direction and mapped divergence at selected SNPs at the population level. Additionally, we identified stream populations with extensive admixture, and we used a model-testing framework to investigate complex demographic histories between the two species. Raw ddRADseq .fastq sequence files, along with intermediate processing files, finalized VCF files, a data summary report, and other data information, are given in the "smb_ddRAD_rawdata.tar file. Metadata, including sample_id, species designation, and stream population, are given in the "metadata.xlsx" file.