Despite considerable effort from the systematics community, delimiting species boundaries in recent radiations remains a daunting challenge. We argue that genealogical approaches, although sometimes useful, may not solve this important problem, because recently derived species often have not had sufficient time to achieve monophyly. Instead, we suggest that population genetic approaches that rely on large sets of informative markers like single nucleotide polymorphisms (SNPs) provide an alternative framework for delimiting very recently derived species. We address two major challenges in applying such markers to species delimitation: discovering markers in nonmodel systems and using them to delimit recently derived species. Using turtles as a test case, we explore the utility of a single, relatively low-coverage genomic resource as an aid in gene and marker discovery. We exploit an end-sequenced bacterial artificial chromosome (BAC) library from an individual painted turtle (Chrysemys picta) and outline a novel protocol that efficiently identifies primer pairs that amplify homologous sequences across the tree of living turtles. Preliminary data using this library to discover SNPs in Emydura macquarii, a species that diverged from C. picta approximately 210 million years ago, indicate that sequences identified from the Chrysemys BAC library provide useful SNPs even in this very distantly related taxon. Several recent methods in wide use in the population genetics literature allow one to discover potential species, or test existing species hypotheses, with SNP data and may be particularly informative for very recently derived species. As BAC and other genomic resources become increasingly available for scattered taxa across the tree of life, we are optimistic that these resources will provide abundant, inexpensive markers that will help delimit boundaries in problematic, recent species radiations.