The goal of this study was to examine the taxonomy, ecology, molecular phylogenetics and biosystematics of two apparently closely related species and to elucidate congruent patterns from these often divergent sub-disciplines of systematics. Phylogenetic analysis of DNA sequences showed that Phacelia fimbriata and Phacelia purshii are sister species that demonstrate species-specific differences in germination but little morphologic or genetic differentiation. While a geographic region of sympatry exists, elevation differences preclude co-occurrence. The widespread P. purshii supports higher levels of morphological and genetic diversity compared to the narrow endemic, P. fimbriata. Gene flow between members of this closely related species pair is blocked by hybrid inviability whose expression occurs following normal pollen tube growth and apparent fertilization. Hybrid seeds are inviable, an effect likely caused by an embryo-endosperm incompatibility that, following fertilization, permits development of maternal, but not hybrid fruit and seed tissues. This reproductive barrier adds to our knowledge of an already diverse suite of isolating mechanisms in Phacelia subgenus Cosmanthus.