Comparative sequencing of the maturase-encoding chloroplast gene matK has great potential for reconstructing phylogenetic relationships not only within families, but also within genera of land plants. This gene of 1550 bp is easily amplified due to highly conserved, flanking coding regions that include the trnK exons, rps 16, and psbA. Several available sequencing primers also have wide applicability. Parsimony analysis of 45 matK sequences representing Saxifragaceae sensu stricto provides a level of resolution comparable to that obtained via chloroplast DNA restriction site analysis. Furthermore, this analysis suggests relationships among genera and species that are highly concordant with the results of separate analyses of rbcL sequences and chloroplast DNA restriction sites, and with those of combined analyses of these three chloroplast DNA data sets. Parsimony analysis of 31 matK sequences representing all six sections of Gilia (Polemoniaceae) and 10 allied genera provides strong evidence for the polyphyly of Gilia and suggests relationships among sections of Gilia that are highly concordant with a recent ITS sequence analysis of the Polemoniaceae. Our analyses suggest that matK sequences are not strongly biased toward transitions, and the frequency of mutations at the first and second codon positions approach the frequency of mutations in the third codon position.