A DNA hybridization phylogeny of four sand dollars using a sea biscuit as an outgroup is presented. The study is unusual in that the normalized percent hybridization (NPH) values were all less than 50%, yet the same topology was obtained regardless of which distance metric was used, i.e., whether reciprocal distances were averaged or not, or whether or not a molecular clock was assumed. The tree also appears robust under jackknifing and bootstrapping. The extent of hybridization between homologous hybrids was measured with a five- to sevenfold higher precision than is typical, and by implication NPH was also measured with a higher than normal precision. The ability to measure highly reproducible NPH values offers the possibility of examining the phylogeny of more widely divergent species than typically studied using DNA hybridization techniques, using 1/NPH as a distance metric. The hypothesis of a molecular clock within the sand dollars was rejected, adding sand dollars to the growing list of groups where significant rate variation is known. A small fraction of the sand dollar genomes hybridized with the distantly related regular sea urchin Lytechinus. These slowly evolving sequences probably represent conserved exonic components of the genome.