Corethrogyne DC. (Asteraceae) is a controversial genus due to complex and confounding variability, and the subject of multiple taxonomic revisions. It was previously included within Lessingia Cham. The single species, C. filaginifolia Nutt., has high infraspecific variability. This study was conducted to better understand this infraspecific variability for C. filaginifolia var. incana (Lindl.) Canby and C. filaginifolia var. linifolia H. M. Hall. Barcoding loci from nuclear ribosomal DNA (nrDNA) and chloroplast DNA (cpDNA) were used along with morphological comparisons of voucher specimens. Based on two nrDNA loci, maximum parsimony, maximum likelihood, and Bayesian analyses, we detected five haplotypes of C. filaginifolia. The two focal varieties of this study, C. filaginifolia var. incana and C. filaginifolia var. linifolia, were indistinguishable at both, nrDNA and cpDNA loci.