Abstract The Arabidopsis thaliana CLAVATA2 (CLV2) gene encodes a leucine-rich repeat protein that regulates the development of the shoot meristem. The levels and patterns of nucleotide variation were assessed for CLV2 and 10 flanking genes that together span a 40-kb region of chromosome I. A total of 296 out of 7959 sequenced nucleotide sites were polymorphic. The mean levels of sequence diversity of the contiguous genes in this region are approximately twofold higher than those of other typical Arabidopsis nuclear loci. There is, however, wide variation in the levels and patterns of sequence variation among the 11 linked genes in this region, and adjacent genes appear to be subject to contrasting evolutionary forces. CLV2 has the highest levels of nucleotide variation in this region, a significant excess of intermediate frequency polymorphisms, and significant levels of intragenic linkage disequilibrium. Most alleles at CLV2 are found in one of three haplotype groups of moderate (>15%) frequency. These features suggest that CLV2 may harbor a balanced polymorphism.