A cDNA sequence that encodes a portion of sunflower (Helianthus annuus L.) seedling isocitrate lyase was selected from a lambda gt11 cDNA library derived from sunflower seedling cotyledon poly(A)(+) messenger RNA. The library was screened for bacteriophage recombinants that expressed antigens which reacted with antisera directed against cotton seed isocitrate lyase. The isolated cDNA hybridized with a 2 kilobase RNA species that was first detectable in maturing sunflower embryos 19 days after flowering and remained at a constant low level through seed desiccation. The prevalence of this transcript in sunflower cotyledons increased by about 10-fold within 2 days after inhibition in darkness, and transcript levels began to decrease by 5 days after imbibtion. During the first 2 days of germination and growth of sunflower seedlings in light, the rate of isocitrate lyase mRNA accumulation was greater than the rate observed during this period in dark-grown seedlings, giving peak levels about 2-fold higher than corresponding levels in dark-grown seedlings. Illumination of seedlings also promoted an earlier, and more rapid decline of isocitrate lyase transcripts. Peak levels of isocitrate lyase mRNA preceded a corresponding peak in immunologically detectable isocitrate lyase polypeptides by about 24 hours. Isocitrate lyase expression in sunflower cotyledons is developmentally regulated and is modulated, in seedlings, by exposure to light. Mechanisms that control these processes appear to function primarily at the level of mRNA accumulation and are likely to involve changes in transcription rates and/or mRNA stability.