Two non-coding DNA regions from both the chloroplast genome (trnL intron, trnL–trnF IGS, trnT–trnL IGS) and nuclear ribosomal genomes (ITS1 and ITS2) were sequenced in the genus Keckiella and allied genera (Penstemon, Chelone, and Nothochelone) to determine which, if any, of these sequences contained sufficient variability to resolve the seven species of Keckiella. The trnL intron contained almost no signal. However, the trnT–trnL chloroplast IGS region and the nuclear ribosomal sequences were capable, to some extent, of resolving the phylogeny of Keckiella. The nrDNA ITS sequences contained slightly more variability than the chloroplast noncoding region. When combined, these non-coding sequences generated a relatively robust and resolved cladogram. Keckiella rothrockii is clearly indicated as the most basal species of the genus, and the remaining taxa appear to belong to two well-supported clades. The first contains the sister taxa K. antirrhinoides and K. cordifolia. The second contains K. breviflora, K. ternata, K. corymbosa, and K. lemmonii. The nodes of the latter three species are not as strongly supported.