Resolving the genealogy of life-the phylogenetic relationships that describe the evolutionary history of species-remains one of the great challenges of systematic biology. The recent proliferation of DNA sequencing technologies has sparked a rapid increase in the volume of genetic data being applied to phylogenetic studies. Single nucleotide polymorphism (SNP) data, ubiquitous genetic markers once considered reserved for population genetic studies, are now being applied in phylogenetics research at deep evolutionary timescales. The potential for SNPs to resolve contentious phylogenetic problems while researchers also investigate population demographics is promising, yet serious challenges remain with respect to data collection, assembly, modeling, and analysis. The low cost and ease of collecting SNPs suggest that they will remain an important source of genetic information for inferring phylogenies across time periods ranging from the Anthropocene to the Cretaceous.