Isochores are large regions of relatively homogeneous nucleotide composition and 
are present in the genomes of all mammals and birds that have been sequenced to 
date. The newly sequenced genome of Anolis carolinensis provides the first 
opportunity to quantify isochore structure in a nonavian reptile. We find Anolis 
to have the most compositionally homogeneous genome of all amniotes sequenced 
thus far, a homogeneity exceeding that for the frog Xenopus. Based on a Bayesian 
algorithm, Anolis has smaller and less GC-rich isochores compared with human and 
chicken. Correlates generally associated with GC-rich isochores, including 
shorter introns and higher gene density, have all but disappeared from the 
Anolis genome. Using genic GC as a proxy for isochore structure so as to compare 
with other vertebrates, we found that GC content has substantially decreased in 
the lineage leading to Anolis since diverging from the common ancestor of 
Reptilia ∼275 Ma, perhaps reflecting weakened or reversed GC-biased gene 
conversion, a nonadaptive substitution process that is thought to be important 
in the maintenance and trajectory of isochore evolution. Our results demonstrate 
that GC composition in Anolis is not associated with important features of 
genome structure, including gene density and intron size, in contrast to 
patterns seen in mammal and bird genomes.