With the draft chicken genome in hand and the draft genomes of Zebra Finch (Taeniopygia guttata) and the Greene Anole lizard (Anolis carolinensis) soon to be released, we are in a position to evaluate the broad differences in the dynamics of genome evolution between mammals on the one hand, and birds and non-avian reptiles on the other. In addition, we have been conducting large-scale end-sequencing of BAC libraries from a tuatara (Sphenodon punctatus), painted turtle (Chrysemys picta), Garter Snake (Thamnophis sirtalis), emu (Dromaius novaehollandiae) and American Alligator (Alligator mississipiensis) in order to add to the DNA sequence resources available for such study. This work suggests that non-avian reptiles possess a rich diversity of chicken-repeat 1 (CR1) family LINE elements and suggests that the ancestral amniote genome was also rich in these repeats, with drastic reductions occurring in the ancestor of extant birds. Using statistical analysis of the frequencies of 8-mer oligonucleotides such as simple-sequence repeats, we find that rates of interspecific oligonucleotide-frequency change in Reptilia are an order of magnitude slower than in mammals. We have begun to annotate extended regions of the major histocompatibility complex (MHC) in Anolis and Zebra Finch, as well as novel BAC sequences from alligator, turtle and emu that have been mapped to both sex chromosomes and autosomes using FISH and in silico. Alignments of these regions to available draft genomes suggest that, despite abundant small-scale intrachromosomal rearrangements, reptile genomies display a conservative mode of evolution commensurate with their slow rates of morphological change compared to mammals.