This project sampled throughout Phacelia using the internal transcribed spacer region (ITS-1, ITS-2, and 5.8S gene) of nuclear ribosomal DNA (nrITS) and the chloroplast DNA gene (ndhF) to infer phylogenies for nuclear and plastid partitions. Nuclear and plastid partitions were incongruent in our analyses. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) recovered gene tree topologies similar to previous molecular studies. We corroborate incongruence between nuclear and plastid topologies for placement of some problematic groups (e.g., Draperia, Romanzoffia and “core” Phacelia subg. Pulchellae, Phacelia sect. Baretiana). Combined analyses resulted in better resolution than separate analyses, and in a topology that favored the separate plastid topologies. Romanzoffia was sister to a monophyletic Phacelia in the combined analyses. Our results support combining incongruent partitions in a combined analysis to seek support for internal nodes. Maximum likelihood analyses were used to infer ancestral chromosome numbers and identify gains, losses, polyploid doubling, and whole genome duplication events from published chromosome counts in the genus. The predicted base number for the genus was x  =  9, x  =  11, or x  =  12.