Agalinis acuta (Orobanchaceae) is a federally listed endangered plant species native to the mid-Atlantic and northeastern coastal plains of the United States. Due to morphological ambiguity and molecular similarity between A. acuta and Agalinis tenella and Agalinis decemloba a conservation priority is to determine whether A. acuta represents an evolutionarily distinct entity worthy of protection under the Endangered Species Act. To resolve this question, a phylogenetic study was first conducted based on seven chloroplast DNA loci and the nuclear DNA locus ITS from 79 individuals representing 29 Agalinis species. A study evaluating the utility of those cpDNA loci and three analytical techniques for the purpose of DNA barcoding was also conducted. The phylogenetic study indicated that A. acuta was perhaps evolutionarily indistinct from A. decemloba and A. tenella. Based on the results of subsequent analyses of 21 microsatellite loci and morphological data evaluated under myriad species concepts, A. acuta, A. decemloba, and A. tenella best represent a single species with two subspecies; the former two putative species would constitute a subspecies called A. decemloba ssp. decemloba and A. tenella would be A. decemloba ssp. tenella.

With evolutionary distinct entities described, a phylogeographic study was conducted to determine the extent to which historical processes rather than contemporaneous events can explain extant patterns of genetic and phenotypic diversity within A. decemloba. The dispersal of a few individuals out of southern refugial populations likely represents the process through which northern populations were established; however, recent anthropogenic effects that disproportionately affected northern populations may have also contributed to extant patterns of diversity. Neutral or adaptive explanations for phenotypic variation among populations are also investigated.

The conservation implications of population genetic analyses were assessed for members of A. decemloba ssp. decemloba. Despite the evidence that this taxon is self-compatible, the high levels of inbreeding and low levels of heterozygosity are of such a magnitude in certain populations that genetic factors may be negatively impacting fitness. Because of the small effective population sizes and degree of isolation, all populations should be managed to reduce the risk of extinction associated with demographic and environmental stochasticity.