Two very different systems of classification of the family Polemoniaceae—one a taxonomic system and the other a molecular cladistic system—have appeared recently. They are compared and reviewed. It is emphasized that taxonomy and cladistics use different basic systematic units (taxa or clades) and have different concepts of monophyly. Furthermore, taxonomy and molecular cladistics differ in the characters used in classification. Conflicts between molecular and reliable morphological characters occur in several parts of the family. The differences in methodology account for most of the incongruences between the two classifications of the family. In general, the methodological differences can be expected to yield incongruences between taxonomic and cladistic systems in any heterogeneous group of medium or large size. New suggestions are made about the early phylogenetic divergences in the Polemoniaceae. The tribes are reviewed from a taxonomic standpoint and a few changes are made.