Noturus stanauli and N. crypticus are two madtom catfish species of conservation concern with very restricted distributions in the Upper Tennessee River Drainage and Duck River. A recent phylogenetic analysis of Noturus using mtDNA sequences did not include these species. A new phylogenetic analysis of cytochrome b sequences including N. stanauli and N. crypticus is presented. Both maximum parsimony and Bayesian analyses indicate that N. stanauli and N. crypticus are closely related and nest within a genetically divergent clade comprising N. fasciatus, N. baileyi, N. elegans, and a paraphyletic N. hildebrandi. Limited intraspecific sampling of N. stanauli and N. crypticus revealed few genetic differences within these species. We discuss our results in the context of conservation status of these species and the use of phylogenetic trees and sequence data in the delimitation of cryptic species diversity in Noturus.