Intraspecific polymorphism of CHLI 2, which codes for subunit I of the Mg-chelatase complex involved in Mg-protoporphyrin IX synthesis, was investigated in 19 ecotypes of Arabidopsis thaliana. Sequence divergence by 35 nucleotides was found. Nucleotide substitutions in 12 out of the 35 positions result in amino acid changes in the functionally significant C-terminal domain of the protein. Of the two divergent sequence haplogroups identified, haplogroup Col displayed an excess of low-frequency polymorphisms, suggesting the effect of purifying selection and a functional significance of CHLI 2. The results suggest a difference in evolutionary dynamics for CHLI 1 and CHLI 2, which determine different forms of subunit I of the Mg-chelatase complex in A. thaliana.