The Perennial Endemic North American clade of Apiaceae (PENA) is the second largest plant group endemic to North America. The large majority of diversity within PENA – 16 genera - is west of the Rocky Mountains, with three genera east of the Mississippi River. The largest genus of the 19 genera within the group, Lomatium, has over 100 species. Some of its widespread taxa lack clear boundaries due to cryptic speciation, convergent evolution, and incomplete lineage sorting – phenomena not uncommon in young lineages such as the PENA clade (molecular dating studies showed that diversification of the clade happened around 2mya). A comprehensive and conclusive phylogenetic hypothesis for the entire clade (containing ~230 taxa) is thus needed. Through intensive collaborative efforts and thorough sampling of every named taxon, in addition to numerous suspected undescribed taxa within PENA and using the next-generation hyb-seq technique, we have been able to sample >300 genes from 400 samples (including all PENA species and multiple individuals from widespread taxa). The concatenated dataset, using maximum likelihood analysis, yielded results that were somewhat congruent with previous analyses. Several clades that were recovered with Sanger sequencing did come out as monophyletic in our analysis, such as the Vesper clade, and the clade we are referring to as the eastern clade (Zizia, Polytaenia, and Thaspium). However, there was poor support at the backbone. Further analyses were done using phased accessions as we suspected high levels of polyploidy within PENA; this second analysis boosted support to a greater extent, especially support at the tips, whereas support at the backbone showed better improvement over non-phased accessions. Efforts are ongoing to construct the multispecies coalescent phylogenetic tree using phased accessions. These efforts will help reconstruct the evolutionary history of this large species-rich clade, resolve where generic and species boundaries may be best drawn, and form the basis for future biogeographic studies.