Variation in breeding systems between species of the same taxonomic group complicates the consistent application of species concepts, and perhaps even the logically consistent circumscription of species. Several genera of arid-zone ephemerals in the Angianthus clade (Asteraceae: Gnaphalieae: Gnaphaliinae) contain both outcrossing and non-outcrossing species. The latter are recognised by producing an order of magnitude fewer pollen grains per anther and an often reduced number of corolla lobes, and they are frequently more widespread than are the former. In its current taxonomy, the genus Pogonolepis comprises an otherwise morphologically indistinguishable pair of one outcrossing and one non-outcrossing species. I generated sequence capture data to test the genetic segregation of P. stricta and P. muelleriana and the utility of sequence capture data for species circumscription and diagnostics. Phylogenetic analysis showed the two species to form two specimen clades, supporting the current taxonomy. Contrary to expectations, non-outcrossing P. muelleriana exhibited lower gene concordance, in line with values expected from recombination, as well as higher heterozygosity than its outcrossing sister species. More research on the breeding system and population structure of the two species may be required to explain these results.