A new and general theory of molecular systematics is emerging, driven by advances in estimating species trees. These trees, which represent lineages, populations, and species rather than genes, are becoming central to phylogenetics, phylogeography, and population genetics. The article argues that species trees should be prioritized as both a practical tool and a long-standing goal in systematics, which has been overshadowed by gene tree analysis. Gene trees are considered a "local optimum" for systematics, but species trees offer a broader, more accurate view. Recent advances in methods, such as coalescent models and multilocus phylogeography, are helping to bridge this gap. The article highlights the importance of distinguishing between gene and species trees, and the need for new methods that account for gene tree heterogeneity. It also discusses the challenges of estimating species trees, including the need for more accurate models and the impact of missing data. The article suggests that the species tree approach is more sensitive to missing data than supermatrix approaches, and that confidence in species trees may be lower than in concatenated analyses, particularly for long-diverged clades. However, the species tree approach is more efficient at extracting information from DNA sequences in some cases. The article concludes that the species tree approach is a promising new direction for molecular systematics, offering a more accurate and comprehensive view of evolutionary history.A new and general theory of molecular systematics is emerging, driven by advances in estimating species trees. These trees, which represent lineages, populations, and species rather than genes, are becoming central to phylogenetics, phylogeography, and population genetics. The article argues that species trees should be prioritized as both a practical tool and a long-standing goal in systematics, which has been overshadowed by gene tree analysis. Gene trees are considered a "local optimum" for systematics, but species trees offer a broader, more accurate view. Recent advances in methods, such as coalescent models and multilocus phylogeography, are helping to bridge this gap. The article highlights the importance of distinguishing between gene and species trees, and the need for new methods that account for gene tree heterogeneity. It also discusses the challenges of estimating species trees, including the need for more accurate models and the impact of missing data. The article suggests that the species tree approach is more sensitive to missing data than supermatrix approaches, and that confidence in species trees may be lower than in concatenated analyses, particularly for long-diverged clades. However, the species tree approach is more efficient at extracting information from DNA sequences in some cases. The article concludes that the species tree approach is a promising new direction for molecular systematics, offering a more accurate and comprehensive view of evolutionary history.