We examined infrageneric relationships within Phacelia subgenus Phacelia based on phylogenetic hypotheses derived from internal transcribed spacers (ITS) and the 5.8S gene of nuclear ribosomal DNA. Maximum parsimony (MP) and maximum likelihood (ML) phylogenies support the monophyly of sects. Euglypta and Miltitzia, previously hypothesized based on seed characters and ecological distribution. Tree branching patterns within the Euglypta/Miltitzia clade indicate three principle lineages: 1) the P. pachyphylla complex, 2) a clade of P. brachyloba and 3) a clade consisting of two sister groups, the P. affinis complex and the P. fremontii complex. An aneuploid increase in chromosome number occurs from the P. pachyphylla complex (n = 11) to P. brachyloba (n = 12) while the pattern within the P. fremontii complex includes both aneuploid increases and decreases. There is high bootstrap support for monophyly of taxa representing both the P. magellanica polyploid complex and the P. humiles species group; the former contains the only known tetraploid taxa in subgenus Phacelia.