摘要The advances accelerated by next-generation se-quencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylo-genetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome se-quencing) in phylogenetic and evolutionary inves-tigations, describes the baseline methodology of experimental and analytical procedures, and sum-marizes recent progress in flowering plant phyloge-nomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic re-construction raised from systematic errors, and un-derlying biological factors, such as whole-genome duplication, hybridization/introgression, and in-complete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.