To circumscribe Saxifragaceae sensu stricto better, as well as to elucidate generic relationships within this group, we sequenced the chloroplast gene rbcL and its 3' flanking region (yielding 1,471 bp) from 19 genera considered to represent core members of Saxifragaceae. In addition, we conducted a restriction site analysis of chloroplast DNA (cpDNA) for 21 core genera using 23 restriction endonucleases. Phylogenetic analyses using both data sets corroborate the results obtained from surveying the distribution of the loss of the intron in the chloroplast gene rp/2 in delimiting a well‐defined Saxifragaceae sensu stricto. Within the Saxifragaceae s.s. clade, a number of poorly resolved, basal phylogenetic branches supports the hypothesis that Saxifragaceae s.s. radiated rapidly very early in its evolutionary history. Molecular data also indicate the presence of several strongly supported groups of genera, such as the Boykinia group (Boykinia, Suksdorfia, Bolandra, Sullivantia, Jepsonia, and Telesonix), the Heuchera group (Heuchera, Bensoniella, Conimitella, Eìmera, Lithophragma, Mitella, Tellima, Tiarelia, and Tolmiea) the Leptarrhena/Tanakaea group, and the Darmera group (Darmera, Astilboides, Mukdenia, Bergenia, and Rodgersia). Significantly, molecular data suggest that the very large, taxonomically complex genus Saxifraga may not be monophyletic. DNA data have also helped to resolve the generic relationships of problematic taxa, indicating, for example, that Telesonix and the enigmatic Jepsonia are sister taxa. In addition to its phylogenetic implications, this study provides insight into basic trends in morphological, chemical, and cytological evolution within Saxifragaceae s.s. The molecular‐based phylogenies suggest multiple origins and/or losses of several classes of flavonoid compounds, as well as several independent instances of reduction in stamen and petal number, hypanthium‐ovary fusion, and aneuploidy. This study also illustrates the ability of rbcL sequence data to resolve generic‐level relationships in some taxonomic groups.
