The cr88 mutant of Arabidopsis is a novel chlorate-resistant mutant that displays long hypocotyls in red light, but not in far red or blue light, and is delayed in the greening process. In cotyledons and young leaves, plastids are less developed compared with those of the wild type. In addition, a subset of light-regulated genes are under-expressed in this mutant. To understand the pleiotropic phenotypes of cr88, we isolated the CR88 gene through map-based cloning. We found that CR88 encodes a chloroplast-targeted 90-kDa heat shock protein (HSP90). The CR88 gene is expressed at highest levels during early post-germination stages and in leaves and reproductive organs. It is constitutively expressed but is also light and heat shock inducible. Chloroplast import experiments showed that the protein is localized to the stroma compartment of the chloroplast. The possible function of an HSP90 in the chloroplast and a plausible explanation of the pleiotropic phenotypes observed in cr88 are discussed.